genesis.pl

#!/usr/bin/perl
#
#	Filename: genesis.pl Version 1.01.300
#	Description: This program accepts a Genesis program 
#		and generates instance programs.
#

use warnings; use strict;

use Scalar::Util qw(looks_like_number);
use File::Copy qw(move);
use File::Compare;
use POSIX;
use Time::HiRes qw/ time sleep /;


#This is needed when using genesis on Linux, maybe?
#$/ = "\r\n";

my $versionnumber = "1.01.300";

##?##?## REGEX SIMPLIFICATIONS ##?##?##
my $interegex= "\^\[\-\]\?\[\\d\]\*";
my $mathregex= "\\\+\\\-\\\*\\\/\\\(\\\)\\\.\\\%";
my $equaregex= "\\w\\\"\\\'$mathregex";
my $ineqregex= "!&\\\|><=\\s$equaregex";
my $referegex= "\\w\\\$\\\{\\\}\\\[\\\]";
my $generegex= "$equaregex$referegex";
my $refqregex= "$referegex$ineqregex";

##?##?## FILENAME VARIABLES ##?##?##
my $filename;   				#the filename of the Genesis program
my $filename2;					#the filename of the template program, if needed
my $outDir = "Gen";				#the directory to put the instance programs
my $outname1 = "gen";			#the format of the instance program 1
my $outname2 = ".c";			#the format of the instance program 2

my $libfilename = "varlist_c.lib";
my $dataoutfilename;			#Outputting the terminal info to a file, if needed
my $dataoutfile;				#the actual dataout handle

##?##?## TIMING VARIABLES ##?##?##
my $starttime = 0;
my $endtime = 0;

my $replacestarttime = 0;
my $replaceendtime = 0;

my $timeparse = 0;
my $timecreate = 0;
my $timereplace = 0;
my $timegen = 0;

##?##?## LINE TYPE COUNTERS ##?##?##
my $constructscount = 0;
my $distscount = 0;
my $valuescount = 0;
my $varlistscount = 0;
my $variablescount = 0;
my $storedscount = 0;
my $addscount = 0;
my $removescount = 0;
my $genmathscount = 0;
my $genassertscount = 0;
my $genifscount = 0;
my $genloopscount = 0;
my $codescount = 0;
my $linescount = 0;
my $replacecount = 0;
my $valreplacecount = 0;
my $varreplacecount = 0;
my $varlistreplacecount = 0;
my $storedreplacecount = 0;
my $featreplacecount = 0;
my $featargreplacecount = 0;
my $genifreplacecount = 0;
my $genloopreplacecount = 0;
my $genloopvarreplacecount = 0;


##?##?## USER INPUTTED FLAGS ##?##?##
my $timingflag = 0;
my $ignorevertspaceflag = 0;		#ignore vertical spacing
my $generateflag = 1; 				#generate at all vs just parse
my $printintroflag = 1;
my $printParsingflag = 2;			#print information during parsing
my $printGenerateflag = 2;			#print information during generation
my $printGlobalcountersflag = 0;	#print global counters of values at the end
my $printerrorsflag = 1;
my $chisquaredtestflag = 0;			#print chi-squared information
my $dtestflag = 0;					#print d information
my $emptyvarlistactionflag = 1;		#control the action when varlist is empty
my $headercommentsflag = 0;			#allow any line in header outside features
my $recursionflag = 0;				#allow feature recursion
my $headerflag = 0;					#make no assumptions about the 
my $referencecheck = 1;				#All references need to be fixed

my $printlocalcountersflag = 0; 	#$#protip: this is broken right now;

##?##?## CONTROL FLOW FLAGS ##?##?##
my $parsingflag = 1;		# Just tells if its parsing or generating
my $samplewarningflag = 0;	# Sampled at end of feature
my $checkoneheaderflag = 0; # A check there is one genesis header
my $badflag = 0;			# Warning redo flag
my $varlistinitflag = 0;	# Initializes the varlists
my $lastlevelflag = 1;		# for proper spacing
my $inagenifflag = 0;		# used for genif/genelsif/genelse
my $genifevaledflag = 0;	# used if a genif is taken
my $varinitflag = 0;		# if 1, init the variables
my $generatetouchflag = 1;  # if 1, touch vars at end
my $valuereportedflag = 0;  # if a value is reported, set to 1
my $distlineflag = 0;		# Helps with distribution removal
my $reportlineflag = 0;		# Adds "Sampled Values" line to header
my $equalWithoutGenmathFlag = 0;
my $referencereplaced = 1;

##?##?## STORAGE VARIABLES ##?##?##
my @globalcodelines;			# Storing the untouched global code lines
my @programcodelines;			# Storing the untouched program code lines
my @templateproglines;			# Storing the untouched target code lines

##?##?## FINAL FILE STORAGE VARIABLES ##?##?##
my @headertemplines;			# Storing the header lines for the final file
my @headerprogramtemplines;		# Storing the header prog lines for the final file 
my @templines;					# Storing the lines for the final file

##?##?## LIBRARY FILE STUFFS ##?##?##
my $reportcharacter = "//"; # Comment character based on instance program file type
my $librarycounter = 0;
my @librarylinename;
my @librarylinefind;
my @librarylinecancel;
my @librarylineactivate;
my @librarylinelocation;
my @librarylineadd;

##?##?## LINE PARSING STORAGE AND USE ##?##?##

##Genesis names
my @namesforlocality;			# List of distribution names for each depth

##Parameters pariter
#  evalflag 1: value name sample parametersdistvar
#  evalflag 0: value name = parametersequalvar
my @parametersnumber;			# Index Number
my @parameters;					# Name of the parameter
my @parametersfeature;			# If in a feature, the feature name
my @parametersdistvar;			# The distribution variable name
my @parametersequalpar;			# The equal parameter name
my @parametersevalflag;			# Eval or =
my @parametersfullflag;			# sample or enumerate
my @parametersreportflag;		# Value modifier: Reporting
my @parametersnoreplaceflag;	# Value modifier: Sampling Replacement
my @parametersarrayflag;		# If this is an array
my @parametersarraybrackets;

my @parameterscounters;			# Counter changes based on depth
my @parameterssampled;			# Sampled?
my @parametersglobalcounter;	# Global counts of values
#my @parametersstartcounter;	#$#protip: this is broken right now;
#my @parameterslocalcounter;	#$#protip: this is broken right now;
my @parametersrealflag;			# If it is a real value
my @parameterschisflag;			# Print the chi squared stats for this value

my @parametersglobalflag;		# Deprecated: Global flag

my @genmathdistvar;

##Varlists vliter
# evalflag 1: varlist varlistname[varlistarg]  <-- sampled varlistarg = distval
# evalflag 0: varlist varlistname = varlistequalvar
my @varlistname;				# Name of the Varlist
my @varlistvarname; 			# Name of the Varlist vars
my @varlistarg;					# The Value Varlist is based on
my @varlistequalvar;			# The equal parameter name
my @varlistevalflag;			# Eval or =
my @varlisttype;				# Varlist modifier: type
my @varlistinitvalue;			# Varlist modifier: init values
my @varlistinitallflag;			# Varlist modifier: initall value
my @varlistendtouch;			# Varlist modifier: endtouch flag

my @varlistvalidity;			# Tells which level the varlist is declared
my @varlistavailability;		# Tells which values in the varlist are available


##Variables variter
# evalflag 1: variable variables from variablesvarlistvar
# evalflag 0: variable variables = variablesequalpar
my @variablesnumber;			# Index Number
my @variables;					# Name of the variable
my @variablesfeature;			# If in a feature, the feature namey
my @variablesvarlistvar;		# Name of the varlist attached
my @variablesequalpar;			# The equal parameter name
my @variablesevalflag;			# Eval or =
my @variablesreportflag;		# Variable modifier: Reporting

my @variablescounters;			# counter changes based on depth

my @variablesglobalflag;		# Deprecated: Global flag


##AddVariables additer
my @addvariablesnumber;			# Index Number
my @addvariables;				# Name of the variable
my @addvariablesvarlistvar;		# Name of the varlist attached
my @addvariablesfeature;		# If in a feature, the feature name

##RemVariables remiter
my @remvariablesnumber;			# Index Number
my @remvariables;				# Name of the variable
my @remvariablesvarlistvar;		# Name of the varlist attached
my @remvariablesfeature;		# If in a feature, the feature name

##Distributions disiter
my @globaldistributions;		# Distributions declared on its own line
my @localdistributions;			# Distributions declared with values = {}
my @distvalidlocality;			# Number indicating which dist index valid at depth

my @distributions;				# Name of the distribution during processing
my @distributionsvalues;		# List of all the values during processing
my @distributionsprob;			# List of all the probabilities during processing
my @distributionsreal;			# If real, how many decimals

##Features feaiter
my @features;					# List of all the feature names
my @featureslist;				# What the feature consists of (the definition)
my @featuresparams;				# List of parameters in declaration
my @featuressinglelineflag; 	# Variable modifier: Reporting

my @featuresparameterlist;		# Stores the parameters passed in during processing
my @featuresparamsvalid;		# Tells that the list is valid
my @featuresvalid;				# Inside a feature. Used to test recursion

my @storednumber;				# Index Number
my @stored;						# Stored feature name
my @storedvar;					# Which feature it is processing from
my @storedfeature;				# Where this is declared (the scope)
my @storedsampled;				# Sampled?

my @storedprocessed;			# Code after it is processed

my @storedglobalflag;			# Deprecated: Global flag	

my $globalexistsflag = 0;		# A global section exists
my @globalenum;					# Which lines have enumerated values
my @globaldist;				# Which lines have distributions
my @globalreport;				# Which lines have reported values
my @globalnames;

my $programexistsflag = 0;		# A program section exists
my @programenum;				# Which lines have enumerated values
my @programdist;				# Which lines have distributions
my @programreport;				# Which lines have reported values
my @programnames;

#genifs
my @genifid;					# Index Number
my @genifinequality;			# Associated variable/inequality
my @geniffeature;				# Which function it is in
my @geniftype;					# Genif, genelsif or genelse
my @geniflist;					# The contents of the genif

#genloops
my @genloopid;					# Index Number
my @genloopvar;					# The loop iterator
my @genloopstart;				# Start value
my @genloopend;					# End value
my @genloopstride;				# Increment
my @genloopinequality;			# Genloop type 2: the inequality
my @genloopvalid;				# Inside a feature. Used to allow loop iterator replacement
my @genloopfeature;				# Which function it is in
my @genlooplist;				# The contents of the genloop

my @genloopvalue;				# Current loop iterator value during processing

#generates
my @generates;					# Number to generate
my @gendistribute;				# Distributions for each generate line
my @gentouch;					# Notouch modifier

##?##?## PARSING FLOW ##?##?##
## counters 
my $linenumber = 0;				# Line number while parsing file
my $valuecounter = 0;			# Current number of Values
my $varlistcounter = 0;			# Current number of Varlists
my $variablecounter = 0;		# Current number of Variables
my $storedcounter = 0;			# Current number of Stored Features
my $addcounter = 0;				# Current number of Adds
my $remcounter = 0;				# Current number of Removes
my $genloopcounter = 0;			# Current number of Genloops
my $genifcounter = 0;			# Current number of Genifs
my $noreplacementcounter = 0;	# Current number of Values with the noreplacement modifier
my $generatecounter = 0;		# Current number of Generates
my $warningcounter = 0;			# Current number of warnings generated
my $setcounter = 0;				# Current number of sets generated
my $dotcounter = 10;			# Output dot counter
my $foldercounter = 1;			# Folder counter

#Parsing variables
my $currentfeature = "";		# Current feature
my @currentgens;				# depth based thing inside brackets
my @currentbracket;				# Things after "genloop"
my @brackettype;				# genif, genloop, etc
my $parsebracketcounter = -1;		# To determine locations of vars
my $genbracketcounter = -1;

##?##?## GENERATING FLOW ##?##?##
my $numtoenumerate = 0;			# Number of enum instances per gen
my $duplicatecounter = 0;		# Counts dups for "too many dup file" warning
my @errorlist;					# Iteration (set) that caused errors 1
my @errorlist2;					# Iteration (enumerate) that caused errors 2
my @warninglist;				# List of warnings

my $currentdepth = 0;			# current depth
my @currentindent;				# spacing changes on depth
$currentindent[0] = "";			# initial state for lineindenting

my @insingleline;
$insingleline[0] = 0;

my $currentreplace = 0;			# check the id for sampling already
my @sampledalready;				# sampled already for noreplace	

##?##?## COMMAND LINE ARGUMENTS ##?##?##

##Varlist arguments
# Name, Doubles counter(set to 0), Duplicate error, Bad value error, Number of possible values, Possible value #1, Possible value #2...
my @varlistarguments = (
["init",     0, "AN", "CB", 0, "Any charstring"],
["initall",  0, "AO", "CC", 0, "Any charstring"],
["type",     0, "AM", "CA", 0, "Any charstring"],
["name",     0, "FB", "FC", 0, "Any charstring"],
["endtouch", 0, "AP", "CD", 2, "1", "0"]
);

##Varlist argument set functions
my %varlistchange = (
 "init"        => sub { $varlistinitvalue[scalar @varlistinitvalue -1] = $_[0]; },
 "initall"     => sub { $varlistinitvalue[scalar @varlistinitvalue -1] = $_[0]; $varlistinitallflag[scalar @varlistinitallflag -1] = 1;},
 "type"        => sub { $varlisttype[scalar @varlisttype -1] = $_[0]; },
 "name"        => sub { $varlistvarname[scalar @varlistvarname -1] = $_[0]; },
 "endtouch"    => sub { $varlistendtouch[scalar @varlistendtouch -1] = $_[0]; }
);

##Value arguments
# Name, Doubles counter(set to 0), Duplicate error, Bad value error, Number of possible values, Possible value #1, Possible value #2...
my @valuearguments = (
["report",        0, "AQ", "CE", 2, "1", "0"],
["noreplacement", 0, "AR", "CF", 2, "1", "0"]
);

##Value argument set functions
my %valuechange = (
 "report"        => sub { $parametersreportflag[scalar @parametersreportflag-1] = $_[0]; if ($_[0] eq "1") {$reportlineflag = 1;}},
 "noreplacement" => sub { if ($_[0] eq "1") {$parametersnoreplaceflag[scalar @parametersnoreplaceflag-1] = $noreplacementcounter;} else {$parametersnoreplaceflag[scalar @parametersnoreplaceflag-1] = 0;} }
);

##Variable arguments
# Name, Doubles counter(set to 0), Duplicate error, Bad value error, Number of possible values, Possible value #1, Possible value #2...
my @vararguments = (
["report", 0, "BC", "CG", 2, "1", "0"]
);

##Variable argument set functions
my %varchange = (
 "report"  => sub { $variablesreportflag[scalar @variablesreportflag-1] = $_[0]; if ($_[0] eq "1") {$reportlineflag = 1;}}
);

##Feature arguments
# Name, Doubles counter(set to 0), Duplicate error, Bad value error, Number of possible values, Possible value #1, Possible value #2...
my @featurearguments = (
["singleline", 0, "AS", "CH", 2, "1", "0"]
);

##Feature argument set functions
my %featurechange = (
 "singleline"        => sub { $featuressinglelineflag[scalar @featuressinglelineflag-1] = $_[0]; }
);

##Command line arguments
# Name, Doubles counter(set to 0), Duplicate error, Bad value error, Number of possible values, Possible value #1, Possible value #2...
my @commandlinearguments = (
["dataoutfile",     0, "EC", "ED", 0, "Any Charstring"],
["outfile",         0, "EE", "EF", -1],
["outdir",          0, "EG", "EH", 0, "Any Charstring"],
["ignorevertspace", 0, "EI", "EJ", 2, "0", "1"],
["generate",        0, "EK", "EL", 2, "1", "0"],
["printParsing",    0, "EM", "EN", 4, "2", "1", "3", "0"],
["printGenerate",   0, "EW", "EX", 4, "2", "1", "3", "0"],
["globalcounters",  0, "EQ", "ER", 2, "0", "1"],
["chisquared",      0, "EU", "EV", 2, "0", "1"],
["headercomments",  0, "EY", "EZ", 2, "0", "1"],
["recursion",       0, "ES", "ET", 2, "1", "0"],
["header",          0, "FA", "DB", 2, "1", "0"],
["seed",            0, "EO", "EP", 0, "a number"]
);

##Command line argument set functions
my %commandlinechange = (
  "dataoutfile"     => sub { $dataoutfilename = $_[0]; },
  "outdir"          => sub { $outDir = $_[0]; },
  "outfile"         => sub { $outname1 = $_[0]; $outname2 = $_[1]; },
  "ignorevertspace" => sub { $ignorevertspaceflag = $_[0]; },
  "generate"        => sub { $generateflag = $_[0]; },
  "printParsing"    => sub { $printParsingflag = $_[0]; },
  "printGenerate"   => sub { $printGenerateflag = $_[0]; },
  "globalcounters"  => sub { $printGlobalcountersflag = $_[0]; },
  "localcounters"   => sub { $printlocalcountersflag = $_[0]; },
  "chisquared"      => sub { $chisquaredtestflag = $_[0]; },
  "headercomments"  => sub { $headercommentsflag = $_[0]; },
  "recursion"       => sub { $recursionflag = $_[0]; },
  "header"          => sub { $headerflag = $_[0]; },
  "seed"            => sub { srand($_[0]); }
);

##?##?## CHI SQUARED VALUE ##?##?##
my @chisquared;				# Calculated chi-squared value for each Gen Value
my @confidenceindex;		# Alpha value for each Gen Value
my @dValue;					# D-value, a different test

##Possible alpha values
my @chisquaredlookupalpha = (100,99,98,97,96,95,94,93,92,91,90,89,88,87,86,85,84,83,82,81,80,79,78,77,76,75,74,73,72,71,70,69,68,67,66,65,64,63,62,61,60,59,58,57,56,55,54,53,52,51,50,49,48,47,46,45,44,43,42,41,40,39,38,37,36,35,34,33,32,31,30,29,28,27,26,25,24,23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0);

##Lookup table
# Sorted by: 
# Each row is a degree of freedom (1d 1st row, 2d 2nd row, etc, up to 200 degrees)
# Each column corresponds to an alpha value (0 to 99, 100 would be infinite)
my @chisquaredlookup = ([0,0.00015709,0.00062845,0.0014144,0.0025154,0.0039321,0.0056656,0.0077167,0.010087,0.012778,0.015791,0.019128,0.022792,0.026784,0.031108,0.035766,0.040761,0.046097,0.051777,0.057805,0.064185,0.070921,0.078019,0.085483,0.093319,0.10153,0.11013,0.11911,0.12849,0.13828,0.14847,0.15909,0.17013,0.18160,0.19352,0.20590,0.21874,0.23206,0.24587,0.26017,0.27500,0.29034,0.30623,0.32268,0.33970,0.35732,0.37554,0.39439,0.41389,0.43407,0.45494,0.47653,0.49886,0.52198,0.54589,0.57065,0.59628,0.62282,0.65032,0.67880,0.70833,0.73894,0.77070,0.80366,0.83789,0.87346,0.91043,0.94890,0.98895,1.0307,1.0742,1.1196,1.1671,1.2167,1.2688,1.3233,1.3806,1.4409,1.5044,1.5714,1.6424,1.7176,1.7976,1.8829,1.9742,2.0723,2.1780,2.2925,2.4173,2.5542,2.7055,2.8744,3.0649,3.2830,3.5374,3.8415,4.2179,4.7093,5.4119,6.6349],
[0,0.020101,0.040405,0.060918,0.081644,0.10259,0.12375,0.14514,0.16676,0.18862,0.21072,0.23307,0.25567,0.27852,0.30165,0.32504,0.34871,0.37266,0.39690,0.42144,0.44629,0.47144,0.49692,0.52273,0.54887,0.57536,0.60221,0.62942,0.65701,0.68498,0.71335,0.74213,0.77132,0.80096,0.83103,0.86157,0.89257,0.92407,0.95607,0.98859,1.0217,1.0553,1.0895,1.1242,1.1596,1.1957,1.2324,1.2698,1.3079,1.3467,1.3863,1.4267,1.4679,1.5100,1.5531,1.5970,1.6420,1.6879,1.7350,1.7832,1.8326,1.8832,1.9352,1.9885,2.0433,2.0996,2.1576,2.2173,2.2789,2.3424,2.4079,2.4757,2.5459,2.6187,2.6941,2.7726,2.8542,2.9394,3.0283,3.1213,3.2189,3.3215,3.4296,3.5439,3.6652,3.7942,3.9322,4.0804,4.2405,4.4145,4.6052,4.8159,5.0515,5.3185,5.6268,5.9915,6.4378,7.0131,7.8240,9.2103],
[0,0.11483,0.18483,0.24510,0.30015,0.35185,0.40117,0.44874,0.49495,0.54009,0.58438,0.62797,0.67101,0.71361,0.75583,0.79777,0.83949,0.88104,0.92248,0.96384,1.0052,1.0465,1.0879,1.1293,1.1709,1.2125,1.2544,1.2963,1.3385,1.3810,1.4237,1.4666,1.5098,1.5534,1.5973,1.6416,1.6862,1.7313,1.7768,1.8227,1.8692,1.9161,1.9636,2.0116,2.0602,2.1095,2.1593,2.2099,2.2612,2.3132,2.3660,2.4196,2.4740,2.5294,2.5857,2.6430,2.7013,2.7608,2.8213,2.8831,2.9462,3.0106,3.0764,3.1437,3.2125,3.2831,3.3554,3.4297,3.5059,3.5842,3.6649,3.7479,3.8336,3.9221,4.0136,4.1083,4.2066,4.3087,4.4150,4.5258,4.6416,4.7630,4.8904,5.0247,5.1665,5.3171,5.4773,5.6489,5.8335,6.0333,6.2514,6.4915,6.7587,7.0603,7.4069,7.8147,8.3112,8.9473,9.8374,11.345],
[0,0.29711,0.42940,0.53505,0.62715,0.71072,0.78837,0.86163,0.93149,0.99865,1.0636,1.1268,1.1884,1.2488,1.3081,1.3665,1.4241,1.4810,1.5374,1.5933,1.6488,1.7040,1.7589,1.8136,1.8681,1.9226,1.9769,2.0313,2.0857,2.1402,2.1947,2.2494,2.3042,2.3593,2.4146,2.4701,2.5259,2.5821,2.6386,2.6955,2.7528,2.8106,2.8689,2.9277,2.9870,3.0469,3.1075,3.1687,3.2306,3.2933,3.3567,3.4209,3.4861,3.5521,3.6191,3.6871,3.7562,3.8265,3.8979,3.9706,4.0446,4.1201,4.1970,4.2755,4.3557,4.4377,4.5216,4.6074,4.6954,4.7857,4.8784,4.9738,5.0719,5.1730,5.2774,5.3853,5.4969,5.6127,5.7329,5.8581,5.9886,6.1251,6.2681,6.4185,6.5770,6.7449,6.9233,7.1137,7.3182,7.5390,7.7794,8.0434,8.3365,8.6664,9.0444,9.4877,10.026,10.712,11.668,13.277],
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[0,152.02,156.62,159.58,161.84,163.69,165.28,166.68,167.94,169.09,170.16,171.15,172.09,172.97,173.81,174.62,175.39,176.13,176.85,177.54,178.21,178.87,179.51,180.13,180.74,181.34,181.93,182.50,183.07,183.63,184.18,184.72,185.26,185.79,186.32,186.84,187.35,187.87,188.38,188.88,189.38,189.88,190.38,190.88,191.37,191.87,192.36,192.85,193.35,193.84,194.33,194.83,195.32,195.82,196.32,196.82,197.32,197.83,198.34,198.85,199.37,199.89,200.42,200.95,201.48,202.03,202.58,203.13,203.70,204.27,204.85,205.45,206.05,206.66,207.29,207.93,208.59,209.26,209.95,210.66,211.40,212.15,212.94,213.75,214.60,215.48,216.41,217.39,218.42,219.52,220.70,221.97,223.36,224.89,226.61,228.58,230.91,233.80,237.67,243.86],
[0,152.90,157.51,160.49,162.75,164.61,166.20,167.61,168.87,170.03,171.09,172.09,173.03,173.91,174.76,175.56,176.34,177.08,177.80,178.50,179.17,179.83,180.47,181.10,181.71,182.31,182.90,183.47,184.04,184.60,185.15,185.70,186.24,186.77,187.30,187.82,188.34,188.85,189.36,189.87,190.37,190.87,191.37,191.87,192.37,192.86,193.36,193.85,194.34,194.84,195.33,195.83,196.33,196.82,197.33,197.83,198.33,198.84,199.35,199.86,200.38,200.91,201.43,201.96,202.50,203.05,203.60,204.16,204.72,205.30,205.88,206.47,207.08,207.69,208.32,208.97,209.62,210.30,210.99,211.70,212.44,213.20,213.98,214.80,215.65,216.54,217.47,218.44,219.48,220.58,221.76,223.04,224.43,225.96,227.69,229.66,232.00,234.89,238.77,244.98],
[0,153.78,158.41,161.39,163.66,165.53,167.12,168.53,169.80,170.96,172.03,173.03,173.97,174.86,175.70,176.51,177.29,178.03,178.75,179.45,180.13,180.79,181.43,182.06,182.67,183.27,183.86,184.44,185.01,185.57,186.13,186.67,187.21,187.75,188.28,188.80,189.32,189.83,190.34,190.85,191.36,191.86,192.36,192.86,193.36,193.85,194.35,194.85,195.34,195.84,196.33,196.83,197.33,197.83,198.33,198.83,199.34,199.85,200.36,200.88,201.40,201.92,202.45,202.98,203.52,204.07,204.62,205.18,205.75,206.32,206.91,207.50,208.11,208.73,209.36,210.00,210.66,211.34,212.03,212.75,213.48,214.24,215.03,215.85,216.70,217.59,218.52,219.50,220.54,221.64,222.83,224.11,225.50,227.04,228.77,230.75,233.09,235.99,239.88,246.09],
[0,154.67,159.31,162.30,164.58,166.44,168.04,169.46,170.73,171.89,172.96,173.97,174.91,175.80,176.65,177.46,178.24,178.99,179.71,180.41,181.09,181.75,182.39,183.02,183.64,184.24,184.83,185.41,185.98,186.55,187.10,187.65,188.19,188.73,189.25,189.78,190.30,190.82,191.33,191.84,192.34,192.85,193.35,193.85,194.35,194.85,195.35,195.84,196.34,196.84,197.33,197.83,198.33,198.83,199.34,199.84,200.35,200.86,201.37,201.89,202.41,202.93,203.46,204.00,204.54,205.09,205.64,206.20,206.77,207.35,207.93,208.53,209.14,209.76,210.39,211.03,211.70,212.37,213.07,213.79,214.52,215.29,216.08,216.90,217.75,218.64,219.57,220.56,221.60,222.71,223.89,225.17,226.57,228.11,229.84,231.83,234.18,237.08,240.98,247.21],
[0,155.55,160.20,163.20,165.49,167.36,168.97,170.38,171.66,172.82,173.90,174.90,175.85,176.74,177.59,178.41,179.19,179.94,180.66,181.36,182.04,182.71,183.35,183.98,184.60,185.21,185.80,186.38,186.95,187.52,188.07,188.62,189.17,189.70,190.23,190.76,191.28,191.80,192.31,192.82,193.33,193.84,194.34,194.84,195.34,195.84,196.34,196.84,197.34,197.84,198.33,198.83,199.33,199.84,200.34,200.85,201.35,201.87,202.38,202.90,203.42,203.95,204.48,205.01,205.56,206.11,206.66,207.22,207.79,208.37,208.96,209.56,210.17,210.79,211.42,212.07,212.73,213.41,214.11,214.83,215.57,216.33,217.12,217.94,218.80,219.69,220.63,221.61,222.66,223.77,224.96,226.24,227.64,229.19,230.92,232.91,235.26,238.18,242.08,248.33],
[0,156.43,161.10,164.11,166.40,168.28,169.89,171.31,172.59,173.76,174.84,175.84,176.79,177.69,178.54,179.36,180.14,180.89,181.62,182.32,183.00,183.67,184.31,184.95,185.57,186.17,186.77,187.35,187.92,188.49,189.05,189.60,190.14,190.68,191.21,191.74,192.26,192.78,193.30,193.81,194.32,194.83,195.33,195.83,196.34,196.84,197.34,197.84,198.33,198.83,199.33,199.83,200.34,200.84,201.35,201.85,202.36,202.88,203.39,203.91,204.43,204.96,205.49,206.03,206.57,207.12,207.68,208.24,208.82,209.40,209.99,210.58,211.20,211.82,212.45,213.10,213.77,214.45,215.15,215.87,216.61,217.37,218.17,218.99,219.85,220.74,221.68,222.67,223.72,224.83,226.02,227.31,228.71,230.26,232.00,233.99,236.35,239.27,243.19,249.44]);

# Clean Exit: For now, remove lingering files
sub cleanexit {
	unlink 'final.c';
}

##?##?## GENERAL PRINTING ##?##?##

# Printing during phase 1, parsing
sub printP {
	my $level = $_[0];
	my $text = $_[1];
	if ($printParsingflag >= $level) {
		print $dataoutfile $text;
	}
}
# Printing during phase 2, generation
sub printG {
	my $level = $_[0];
	my $text = $_[1];
	if (($printGenerateflag != 2 || $level != 0) && $printGenerateflag > 0 && $printGenerateflag >= $level) {
		print $dataoutfile $text;
	}
}
# Error printing. Exits the program when hit.
sub printerror {
	my $code = $_[0];
	my $errorlinenumber = $_[1];
	my $text = $_[2];
	my $message = $_[3];
		
	if ($printerrorsflag != 0) {
		print "\n";
		if ($parsingflag == 1) {
			print "Error Code $code at line $linenumber: '$text'\n";
			print "$message\n";
		}
		elsif ($errorlinenumber ne "" && numbervsstring($errorlinenumber) == 1) {
			print "Error Code $code at line $errorlinenumber: '$text'\n";
			print "$message\n";
		}
		else {
			print "Error Code $code while working with: '$text'\n";
			print "$message\n";
		}
		cleanexit();
		exit;
	}
}
# Warning printing. Can still continue processing.
sub printwarning {
	my $code = $_[0];
	my $errorlinenumber = $_[1];
	my $text = $_[2];
	my $message = $_[3];
	
	if ($printerrorsflag != 0) {
		print "\n";	
		my $fullmessage;
		if ($parsingflag == 1) {
			$fullmessage = "Warning Code $code at line $linenumber: '$text'. " . "$message\n";
		}
		elsif ($errorlinenumber ne "" && numbervsstring($errorlinenumber) == 1) {
			$fullmessage = "Warning Code $code at line $errorlinenumber: '$text'. " . "$message\n";
		}
		else {
			$fullmessage = "Warning Code $code while working with: '$text'. " . "$message\n";
		}
		print $fullmessage;
		$warningcounter++;
		$warninglist[scalar @warninglist] = $fullmessage;
	}
}

##?##?## PRINT SUMMARY STUFF ##?##?##

# PARSING PHASE: Print values, varlists, variables, add and removes
sub printParameters {
	printP (1, "Print Parameters!\n");
	printP (1, "Size of Parametersnumber:        '". scalar @parametersnumber. "'\n");
	printP (1, "Size of Parameters:              '". scalar @parameters. "'\n");
	printP (1, "Size of ParametersFeature:       '". scalar @parametersfeature. "'\n");
	printP (1, "Size of ParametersDistVar:       '". scalar @parametersdistvar. "'\n");
	printP (1, "Size of ParametersEqualPar:      '". scalar @parametersequalpar. "'\n");
	printP (1, "Size of ParametersEvalFlag:      '". scalar @parametersevalflag. "'\n");
	printP (1, "Size of ParametersFullFlag:      '". scalar @parametersfullflag. "'\n");
	printP (1, "Size of parametersReportFlag:    '". scalar @parametersreportflag. "'\n");
	printP (1, "Size of parametersNoReplaceFlag: '". scalar @parametersnoreplaceflag. "'\n\n");

	for(my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		printP (1, " Parameter $parametersnumber[$pariter]:              '". $parameters[$pariter]. "'\n");
		printP (1, "  parametersfeature:       '". $parametersfeature[$pariter]. "'\n");
		printP (1, "  parametersdistvar:       '". $parametersdistvar[$pariter]. "'\n");
		printP (1, "  parametersequalpar:      '". $parametersequalpar[$pariter]. "'\n");
		printP (1, "  parametersevalflag:      '". $parametersevalflag[$pariter]. "'\n");
		printP (1, "  parametersfullflag:      '". $parametersfullflag[$pariter]. "'\n");
		printP (1, "  parametersreportflag:    '". $parametersreportflag[$pariter]. "'\n");
		printP (1, "  parametersnoreplaceflag: '". $parametersnoreplaceflag[$pariter]. "'\n\n");
		
	}
	
	
	printP (1, "\nPrint VarList!\n");
	printP (1, "Size of VarListName:         '". scalar @varlistname. "'\n");
	printP (1, "Size of VarListVarName:      '". scalar @varlistvarname. "'\n");
	printP (1, "Size of VarListArg:          '". scalar @varlistarg. "'\n");
	printP (1, "Size of VarListequalvar:     '". scalar @varlistequalvar. "'\n");
	printP (1, "Size of VarListevalflag:     '". scalar @varlistevalflag. "'\n");
	printP (1, "Size of VarListType:         '". scalar @varlisttype. "'\n");
	printP (1, "Size of VarListInitValue:    '". scalar @varlistinitvalue. "'\n");
	printP (1, "Size of VarListinitallflag:  '". scalar @varlistinitallflag. "'\n");
	printP (1, "Size of VarListendtouch:     '". scalar @varlistendtouch. "'\n\n");
	
	for(my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
		printP (1, " varlistname:          '". $varlistname[$vliter]. "'\n");
		printP (1, "  varlistarg:          '". $varlistarg[$vliter]. "'\n");
		printP (1, "  varlistequalvar      '". $varlistequalvar[$vliter]. "'\n");
		printP (1, "  varlistevalflag:     '". $varlistevalflag[$vliter]. "'\n");
		printP (1, "  varlisttype:         '". $varlisttype[$vliter]. "'\n");
		printP (1, "  varlistinitvalue:    '". $varlistinitvalue[$vliter]. "'\n");
		printP (1, "  varlistinitallflag:  '". $varlistinitallflag[$vliter]. "'\n");
		printP (1, "  varlistendtouch:     '". $varlistendtouch[$vliter]. "'\n");
	}
	
	
	printP (1, "\nPrint Variables!\n");
	printP (1, "Size of VariablesNumber:     '". scalar @variablesnumber. "'\n");
	printP (1, "Size of Variables:           '". scalar @variables. "'\n");
	printP (1, "Size of variablesVarlistVar: '". scalar @variablesvarlistvar. "'\n");
	printP (1, "Size of variablesEqualPar:   '". scalar @variablesequalpar. "'\n");
	printP (1, "Size of variablesEvalflag:   '". scalar @variablesevalflag. "'\n");
	printP (1, "Size of variablesreportflag: '". scalar @variablesreportflag. "'\n");
	printP (1, "Size of variablesFeature:    '". scalar @variablesfeature. "'\n\n");

	for(my $variter = 0; $variter < scalar @variables; $variter++) {
		printP (1, " Variable $variablesnumber[$variter]:           '". $variables[$variter]. "'\n");
		printP (1, "  variablesvarlistvar: '". $variablesvarlistvar[$variter]. "'\n");
		printP (1, "  variablesequalpar:   '". $variablesequalpar[$variter]. "'\n");
		printP (1, "  variablesevalflag:   '". $variablesevalflag[$variter]. "'\n");
		printP (1, "  variablesreportflag: '". $variablesreportflag[$variter]. "'\n");
		printP (1, "  variablesfeature:    '". $variablesfeature[$variter]. "'\n\n");
	}
	
	printP (1, "\nPrint AddVariables!\n");
	printP (1, "Size of AddVariablesNumber:  '". scalar @addvariablesnumber. "'\n");
	printP (1, "Size of AddVariables:        '". scalar @addvariables. "'\n");
	printP (1, "Size of AddVariablesDistVar: '". scalar @addvariablesvarlistvar. "'\n");
	printP (1, "Size of AddVariablesFeature: '". scalar @addvariablesfeature. "'\n\n");
	
	for(my $additer = 0; $additer < scalar @addvariables; $additer++) {
		printP (1, " addvariables $addvariablesnumber[$additer]:          '". $addvariables[$additer]. "'\n");
		printP (1, "  addvariablesvarlistvar: '". $addvariablesvarlistvar[$additer]. "'\n");
		printP (1, "  addvariablesfeature:    '". $addvariablesfeature[$additer]. "\n\n");
	}
	
	printP (1, "\nPrint RemVariables!\n");
	printP (1, "Size of RemVariablesNumber:  '". scalar @remvariablesnumber. "'\n");
	printP (1, "Size of RemVariables:        '". scalar @remvariables. "'\n");
	printP (1, "Size of RemVariablesDistVar: '". scalar @remvariablesvarlistvar. "'\n");
	printP (1, "Size of RemVariablesFeature: '". scalar @remvariablesfeature. "\n\n");

	for(my $remiter = 0; $remiter < scalar @remvariables; $remiter++) {
		printP (1, " remvariables $remvariablesnumber[$remiter]:          '". $remvariables[$remiter]. "'\n");
		printP (1, "  remvariablesvarlistvar: '". $remvariablesvarlistvar[$remiter]. "'\n");
		printP (1, "  remvariablesfeature:    '". $remvariablesfeature[$remiter]. "'\n\n");
	}
	

}
# PARSING PHASE: Print generate statements
sub printGenerates {	
	printP (1, "Print Distributions!\n");
	printP (1, "Size of globaldistributions:     ". scalar @globaldistributions. "\n");
	printP (1, "Size of localdistributions:     ". scalar @localdistributions. "\n");

	for(my $disiter = 0; $disiter < scalar @globaldistributions; $disiter++) {
		printP (1, " GlobalDistribution $disiter: ". $globaldistributions[$disiter]. "\n");
	}	
	
	for(my $disiter = 0; $disiter < scalar @localdistributions; $disiter++) {
		printP (1, " LocalDistribution $disiter: ". $localdistributions[$disiter]. "\n");
	}	
	
	printP (1, "Size of generates:     ". scalar @generates. "\n");
	printP (1, "Size of gendistribute: ". scalar @gendistribute. "\n");
	printP (1, "Size of gentouch:      ". scalar @gentouch. "\n");
	for(my $disiter = 0; $disiter < scalar @generates; $disiter++) {
		printP (1, " generates:     ". $generates[$disiter]. "\n");
		printP (1, " gendistribute: ". $gendistribute[$disiter]. "\n");
		printP (1, " gentouch:      ". $gentouch[$disiter]. "\n");
	}
}
# PARSING PHASE: Print global, program, features, genif and genloops
sub printFeatures {
	printP (1, "\nPrint features!\n");
	
	printP (1, "Size of Global:                ". scalar @globalcodelines. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @globalcodelines; $feaiter++) {
		printP (1, "  Global line $feaiter: $globalcodelines[$feaiter]");
	}
	
	printP (1, "Size of Global Enum:           ". scalar @globalenum. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @globalenum; $feaiter++) {
		printP (1, "  Global enum line $feaiter: $globalenum[$feaiter]\n");
	}
	printP (1, "Size of Global Report:         ". scalar @globalreport. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @globalreport; $feaiter++) {
		printP (1, "  Global report line $feaiter: $globalreport[$feaiter]\n");
	}
	
	
	
	printP (1, "Size of Program:               ". scalar @programcodelines. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @programcodelines; $feaiter++) {
		printP (1, "  Program line $feaiter: $programcodelines[$feaiter]");
	}
	
	printP (1, "Size of Program Enum:          ". scalar @programenum. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @programenum; $feaiter++) {
		printP (1, "  Program enum line $feaiter: $programenum[$feaiter]\n");
	}
	
	printP (1, "Size of Program Dist:          ". scalar @programdist. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @programdist; $feaiter++) {
		printP (1, "  Program dist line $feaiter: $programdist[$feaiter]\n");
	}
	
	printP (1, "Size of Program Report:        ". scalar @programreport. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @programreport; $feaiter++) {
		printP (1, "  Program report line $feaiter: $programreport[$feaiter]\n");
	}
	
	printP (1, "Size of Features:              ". scalar @features. "\n");
	printP (1, "Size of FeaturesList:          ". scalar @featureslist. "\n");
	printP (1, "Size of FeatureParams:         ". scalar @featuresparams. "\n");
	printP (1, "Size of Featureparameterlist:  ". scalar @featuresparameterlist. "\n");
	printP (1, "Size of Featuresinglelineflag: ". scalar @featuressinglelineflag. "\n");
	printP (1, "Size of Featureparamsvalid:    ". scalar @featuresparamsvalid. "\n");

	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
		printP (1, "Feature #$feaiter: " . $features[$feaiter] . "\n");
		printP (1, "  with " . scalar @{$featuresparams[$feaiter]} . " Params and " . scalar @{$featureslist[$feaiter]} . " feature lines\n");
		for (my $funiter = 0; $funiter < scalar @{$featureslist[$feaiter]}; $funiter++) {
			printP (1, "   Feature line $funiter: ${$featureslist[$feaiter]}[$funiter]");
		}
		for (my $pariter = 0; $pariter < scalar @{$featuresparams[$feaiter]}; $pariter++) {
			printP (1, "  Param: ${$featuresparams[$feaiter]}[$pariter]\n");
		}
		for (my $pariter = 0; $pariter < scalar @{$featuresparameterlist[$feaiter]}; $pariter++) {
			printP (1, "  Paramlist: ${$featuresparameterlist[$feaiter]}[$pariter]\n");
		}
		printP (1, "featuressinglelineflag: '$featuressinglelineflag[$feaiter]'\n");
		printP (1, "featuresparamsvalid: '$featuresparamsvalid[$feaiter]'\n\n");
	}
	printP (1, "Size of Stored:              ". scalar @stored. "\n");
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @stored; $feaiter++) {
		printP (1, "Feature #$feaiter: " . $stored[$feaiter] . "\n");
	}
	
	printP (1, "\nPrint genifs!\n");
	printP (1, "Size of GenifID: ". scalar @genifid. "\n");
	printP (1, "Size of genifinequality: ". scalar @genifinequality. "\n");
	printP (1, "Size of GenifFunction: ". scalar @geniffeature. "\n");
	printP (1, "Size of GenifList: ". scalar @geniflist. "\n");
	printP (1, "Size of GenifType: ". scalar @geniftype. "\n");
	
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @genifinequality; $feaiter++) {
		printP (1, "Genif #$genifid[$feaiter]: \n");
		printP (1, " genifinequality: '$genifinequality[$feaiter]'\n");
		printP (1, " geniffeature:    '$geniffeature[$feaiter]'\n");
		printP (1, " geniftype:       '$geniftype[$feaiter]'\n");
		printP (1, " geniflist:       '". scalar @{$geniflist[$feaiter]} ."'\n");
		for (my $funiter = 0; $funiter < scalar @{$geniflist[$feaiter]}; $funiter++) {
			printP (1, "Genif line $funiter: ${$geniflist[$feaiter]}[$funiter]");
		}
		printP (1, "\n");
	}
	
	printP (1, "\nPrint genloops!\n");
	printP (1, "Size of GenloopID: ". scalar @genloopid. "\n");
	printP (1, "Size of GenloopVar: ". scalar @genloopvar. "\n");
	printP (1, "Size of GenloopStart: ". scalar @genloopstart. "\n");
	printP (1, "Size of GenloopEnd: ". scalar @genloopend. "\n");
	printP (1, "Size of GenloopStride: ". scalar @genloopstride. "\n");
	printP (1, "Size of GenloopValid: ". scalar @genloopvalid. "\n");
	printP (1, "Size of GenloopValue: ". scalar @genloopvalue. "\n");
	printP (1, "Size of GenloopFeature: ". scalar @genloopfeature. "\n");
	printP (1, "Size of GenloopList: ". scalar @genlooplist. "\n");
		
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @genloopvar; $feaiter++) {
		printP (1, "Genloop #$genloopid[$feaiter]: \n");
		printP (1, " genloopvar:        '$genloopvar[$feaiter]'\n");
		printP (1, " genloopstart:      '$genloopstart[$feaiter]'\n");
		printP (1, " genloopend:        '$genloopend[$feaiter]'\n");
		printP (1, " genloopstride:     '$genloopstride[$feaiter]'\n");
		printP (1, " genloopvalid:      '$genloopvalid[$feaiter]'\n");
		printP (1, " genloopvalue:      '$genloopvalue[$feaiter]'\n");
		printP (1, " genloopfeature:    '$genloopfeature[$feaiter]'\n");
		printP (1, " genlooplist:       '". scalar @{$genlooplist[$feaiter]} ."'\n");
		for (my $funiter = 0; $funiter < scalar @{$genlooplist[$feaiter]}; $funiter++) {
			printP (1, "Genloop line $funiter: '${$genlooplist[$feaiter]}[$funiter]'");
		}
		printP (1, "\n");
	}
	
}
# PARSING PHASE: Top level print all
sub printeverything {
	printP (1, "\n\nPrint everything!\n");
	printParameters();
	printGenerates();
	printFeatures();
	printP (1, "\nEnd Print everything!\n\n");
}

# GENERATION PHASE: Print Final Report
sub printfinalreport {
	my $generated = $generatecounter - scalar @errorlist;
	my $failed = scalar @errorlist;
	printG (1, "Final Report!\n");
	#Generated how many files
	if ($generated == 1) {
		printG (1, " Generated $generated instance programs");
	}
	else {
		printG (1, " Generated $generated instance programs");
	}
	if (scalar @programenum > 0) {
		if ($setcounter == 1) {
			printG (1, " in $setcounter set");
		}
		else {
			printG (1, " in $setcounter sets");
		}
	}
	#Warnings summary
	if ($warningcounter > 0) {
		printG (1, " with $warningcounter warnings\n");
	}
	for (my $i = 0; $i < scalar @warninglist; $i++) {
		printG (1, "  Warning message: $warninglist[$i]");
	}
	printG (1, ".\n");
	#Errors summary
	if ($failed == 1) {
		printG (1, " $failed file failed to generate.\n");
	}
	elsif ($failed != 0) {
		printG (1, " $failed files failed to generate.\n");
	}
	else {
		printG (1, " All files successfully generated.\n");
	}
	for (my $i = 0; $i < scalar @errorlist; $i++) {
		printG (1, "  File Failed: ". $outname1.$errorlist[$i]."_".$errorlist2[$i].$outname2."\n");
	}
	
	if ($timingflag == 1) {
		print "Time in parsing: $timeparse\n";
		print "Time in generating: $timecreate\n";
		print " Time in replacement: $timereplace\n";
		print "Time in printing to file: $timegen\n";
		print "# of constructs: $constructscount\n";
		print " # of dists: $distscount\n";
		print " # of values: $valuescount\n";
		print " # of varlists: $varlistscount\n";
		print " # of variables: $variablescount\n";
		print " # of stored: $storedscount\n";
		print " # of adds: $addscount\n";
		print " # of removes: $removescount\n";
		print " # of genmaths: $genmathscount\n";
		print " # of genasserts: $genassertscount\n";
		print " # of genifs: $genifscount\n";
		print " # of genloops: $genloopscount\n";
		print "# of codes: $codescount\n";
		print "# of total lines: $linescount\n";
		print "# of replaces: $replacecount\n";
		print " # of value replaces: $valreplacecount\n";
		print " # of variable replaces: $varreplacecount\n";
		print " # of varlist replaces: $varlistreplacecount\n";
		print " # of stored replaces: $storedreplacecount\n";
		print " # of feature replaces: $featreplacecount\n";
		print " # of feature arg replaces: $featargreplacecount\n";
		print " # of genif replaces: $genifreplacecount\n";
		print " # of genloop replaces: $genloopreplacecount\n";
		print " # of genloopvar replaces: $genloopvarreplacecount\n";
	}
	
}
sub lineCount {
	my $type = $_[0];
	if ($timingflag == 1) {
		if ($type <= 13) {
			$linescount++;
			if ($type == 12) {
				$codescount++;
			}
			else {
				$constructscount++;
				if ($type == 1) {
					$distscount++;
				}
				elsif ($type == 2) {
					$valuescount++;
				}
				elsif ($type == 3) {
					$varlistscount++;
				}
				elsif ($type == 4) {
					$variablescount++;
				}
				elsif ($type == 5) {
					$storedscount++;
				}
				elsif ($type == 6) {
					$addscount++;
				}
				elsif ($type == 7) {
					$removescount++;
				}
				elsif ($type == 8) {
					$genmathscount++;
				}
				elsif ($type == 9) {
					$genassertscount++;
				}
				elsif ($type == 10) {
					$genifscount++;		
				}
				elsif ($type == 11) {
					$genloopscount++;
				}
			}
		}
		else {
			$replacecount = 0;
			if ($type == 14) {
				$valreplacecount++;
			}
			elsif ($type == 15) {
				$varreplacecount++;
			}
			elsif ($type == 16) {
				$varlistreplacecount++;
			}
			elsif ($type == 17) {
				$storedreplacecount++;
			}
			elsif ($type == 18) {
				$featreplacecount++;
			}
			elsif ($type == 19) {
				$featargreplacecount++;
			}
			elsif ($type == 20) {
				$genifreplacecount++;
			}
			elsif ($type == 21) {
				$genloopreplacecount++;
			}
			elsif ($type == 22) {
				$genloopvarreplacecount++;
			}
		}
	}
}

##?##?## FOR DEBUGGING PRINTING DURING PROCESSING ##?##?##

# Print current parameter set
sub debug_printcurrentparameterset {
	for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		print "$parameters[$pariter]:\n";
		for (my $i = 0; $i < $currentdepth; $i++) {

			printd (2, " $i: ${$parameterscounters[$i]}[$pariter]\n");
		}
		
	}
}
# Print distributions after they are parsed
sub debug_printdistributions {
	printP (1, "Print Distributions!!!\n");
	printP (1, "Size of Distributions: ". scalar @distributions. "\n");
	printP (1, "Size of DistributionCounter: ". scalar @distributionsvalues. "\n");
	printP (1, "Size of DistributionProb: ". scalar @distributionsprob. "\n");
	printP (1, "Size of DistributionReal: ". scalar @distributionsreal. "\n");

	
	for(my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
		printP (1, " Distribution: ". $distributions[$disiter]. "\n");
		printP (1, " Size of DistributionCounter[$disiter]: ". scalar @{$distributionsvalues[$disiter]}. "\n");
		printP (1, " Size of DistributionProb[$disiter]: ". scalar @{$distributionsprob[$disiter]}. "\n");
		for(my $j = 0; $j < scalar @{$distributionsvalues[$disiter]}; $j++) {
			printP (1, "		Range: '" . ${$distributionsvalues[$disiter]}[$j] ."' with Distribution: '" . ${$distributionsprob[$disiter]}[$j] .  "and ${$distributionsprob[$disiter]}[$j] '\n");
			
		}
	}	
}
# Print the status of the varlist and which are allowed
sub debug_printvarlists {
	printG (3, "Begin var avail$_[0]\n");
	for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
		printG (3, "$varlistname[$vliter]: ");
		for (my $variter2 = 0; $variter2 < scalar @{$varlistavailability[$vliter]}; $variter2++) {
			printG (3, "${$varlistavailability[$vliter]}[$variter2]");
		}
		printG (3, "\n");
	}
	printG (3, "End var avail$_[0]\n");
}
# Print the parameters that were passed into a feature
sub debug_printParams {
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
		print "Feature $feaiter $features[$feaiter] with $featuresparamsvalid[$feaiter]\n";
		for (my $pariter = 0; $pariter < $featuresparamsvalid[$feaiter]; $pariter++) {
			print " $pariter ${${$featuresparameterlist[$feaiter]}[$pariter]}[0]\n";
		}
	}
}
# Print the list of currently used Genesis names (names that cannot be reused)
sub debug_printlocalitynames {
	print "BC: $parsebracketcounter ";
	print scalar @{$namesforlocality[$parsebracketcounter+1]};
	for (my $i = 0; $i <= $parsebracketcounter; $i++) {
		for (my $j = 0; $j < scalar @{$namesforlocality[$i]}; $j++) {
		
			print "$i $j = ${$namesforlocality[$i]}[$j]\n";
		}
		
	}
	print "\n";
}

##?##?## VALUE COUNTER MANIPULATION ##?##?##

# GENERATION PHASE: Initiate all global counters to 0
sub setupGlobalCounters {
	for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		my @parametersglobalcounters;
		for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
			if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {
				for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]}; $disiter2++) {
					$parametersglobalcounters[$disiter2] = 0;
				}
			}
		}
		$parametersglobalcounter[$pariter] = \@parametersglobalcounters;
	}
}
# GENERATION PHASE: Print the global counters and performs the chi squared test
sub printParamglobalcounters {
	if ($printGlobalcountersflag == 1 || $chisquaredtestflag == 1) {
		print "Global Parameter counters: \n";
		for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
			if ($parametersevalflag[$pariter] == 1 && $parametersfullflag[$pariter] == 0 && $parametersrealflag[$pariter] == 0) {
				$parameterschisflag[$pariter] = 1;
				print " $parameters[$pariter] \n";
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {
						for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]}; $disiter2++) {
							print "  value ${$distributionsvalues[$disiter]}[$disiter2]: ${$parametersglobalcounter[$pariter]}[$disiter2]\n";
						}
						if ($chisquaredtestflag == 1) {
							#Perform the chi squared test
							chiSquaredTest ($pariter);
						}
					}
				}
				
			}
			else {
				$parameterschisflag[$pariter] = 0;
			}

		}
		#Displays a chi squared test summary
		if ($chisquaredtestflag == 1) {
			print "Test Summary \n";
			my $counter = 0;
			for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
				if ($parameterschisflag[$pariter] == 1){
					my $alpha1 = $chisquaredlookupalpha[$confidenceindex[$counter]]/100;
					my $alpha2 = $chisquaredlookupalpha[$confidenceindex[$counter]-1]/100;
					my $differs1 = (100-$chisquaredlookupalpha[$confidenceindex[$counter]-1]);
					my $differs2 = (100-$chisquaredlookupalpha[$confidenceindex[$counter]]);
					
					print " For $parameters[$pariter] | Chi2: $chisquared[$counter] | Alpha: $alpha1-$alpha2 | Differs from declared: $differs1\%-$differs2\%";
					if ($dtestflag == 1) {
					print " | D: $dValue[$counter] ";
					}
					print "\n";
					$counter++;
				}
			}
		}
		
	}
}
# CLEANUP PHASE: Perform the chi-squared test on a single parameter
sub chiSquaredTest {
	my $pariter = $_[0];
	my $sum = 0;
	my @expected;
	my @expectedrounded;
	my @colD;
	my @colE;
	my @colF;
	my $finalchisquaredvalue = 0;
	
	my $actualsum = 0;
	my $expectedsum = 0;
	my $currentDvalue = 0;
	my $Pvalue = 0;
	print "\n";
	print "Chi Squared Test\n";
	print "for $parameters[$pariter] \n";
	
	#Find the distribution that corresponds to the parameter
	for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
		if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {
			
			#make sure there is at least 1 sample
			for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]}; $disiter2++) {
				$sum = $sum + ${$parametersglobalcounter[$pariter]}[$disiter2];
			}
			if ($sum > 0) {
			
				#fill out the table
				for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]}; $disiter2++) {
					$expected[scalar @expected] = ${$distributionsprob[$disiter]}[$disiter2]*$sum;
					$expectedrounded[scalar @expectedrounded] = sprintf "%.2f   ", $expected[$disiter2];
					
					$colD[scalar @colD] = ${$parametersglobalcounter[$pariter]}[$disiter2]-$expected[$disiter2];
					$colE[scalar @colE] = $colD[$disiter2]*$colD[$disiter2];
					$colF[scalar @colF] = $colE[$disiter2]/$expected[$disiter2];
				}

				
				print " ColA: Value\n";
				print " ColB: Actual Count\n";
				print " ColC: Expected Count\n";
				print " ColD: ColB-ColC\n";
				print " ColE: ColD Squared\n";
				print " ColF: ColE/ColC\n";
				print "\n";
				print "        A     B      C        D       E      F\n";
				for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]}; $disiter2++) {
					$finalchisquaredvalue = $finalchisquaredvalue + $colF[$disiter2];
				
					print "  value ${$distributionsvalues[$disiter]}[$disiter2]:   ${$parametersglobalcounter[$pariter]}[$disiter2]   ";
					
					
					printf "%.2f   ", $expectedrounded[$disiter2];
					printf "%.2f   ", $colD[$disiter2];
					printf "%.2f   ", $colE[$disiter2];
					printf "%.2f\n", $colF[$disiter2];
				}
				
				#Final Chi Squared value for this parameter
				$chisquared[scalar @chisquared] = sprintf "%.2f", $finalchisquaredvalue;
				print "Final Chi Squared Value: $finalchisquaredvalue\n";
				print "\n";
				print "\n";
				
				#Degrees of freedom to use the lookup table
				my $dof = scalar @{$distributionsvalues[$disiter]} - 1;
				
				#Find what alpha this corresponds to (between)
				my $found = 0;
				for (my $alphavalue = 0; $found == 0 && $alphavalue < scalar @chisquaredlookupalpha - 1; $alphavalue++) {
					if ($chisquaredlookup[$dof-1][$alphavalue] > $chisquared[scalar @chisquared -1]) {
						@confidenceindex[scalar @confidenceindex] = $alphavalue;
						$found = 1;
					}
				
				}
				if ($found == 0) {
					@confidenceindex[scalar @confidenceindex] = scalar @chisquaredlookupalpha - 1;
				}
				my $alpha1 = $chisquaredlookupalpha[$confidenceindex[scalar @confidenceindex-1]]/100;
				my $alpha2 = $chisquaredlookupalpha[$confidenceindex[scalar @confidenceindex-1]-1]/100;
				my $differs1 = (100-$chisquaredlookupalpha[$confidenceindex[scalar @confidenceindex-1]-1]);
				my $differs2 = (100-$chisquaredlookupalpha[$confidenceindex[scalar @confidenceindex-1]]);
				print " The chi-squared value is between an alpha value of $alpha1 and $alpha2. This means this distribution differs from the declared distribution by between $differs1\% and $differs2\%. ";
				if ($alpha1 < 0.05) {
					print "This means it could still be sampled correctly, but there is a high chance of bias affecting the sampling. \n";
				}
				else {
					print "This means there is no reason to believe it was not sampled correctly. An alpha value below 0.05 would mean there is a high chance of biased.\n\n";
				}
				if ($dtestflag == 1) {
					#A different test: Cumulative Distribution Function test 
					#AKA Kolmogorov Smirnov test, partially implemented
					for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]}; $disiter2++) {			
						$actualsum = $actualsum + ${$parametersglobalcounter[$pariter]}[$disiter2];
						$expectedsum = $expectedsum + $expectedrounded[$disiter2];
						if ($expectedsum-$actualsum > $currentDvalue) {
							$currentDvalue = $expectedsum-$actualsum;
						}
						if ($actualsum-$expectedsum > $currentDvalue) {
							$currentDvalue = $actualsum-$expectedsum;
						}
					}
					#normalize /1
					$currentDvalue = $currentDvalue/$sum;
					$dValue[scalar @dValue] = $currentDvalue;
					print "D = $currentDvalue\n\n";
					#my $s = $sum*$currentDvalue^2;
					#$Pvalue = 2*exp(-(2.000071+.331/sqrt($sum)+1.409/$sum)*$s);
					#http://mathworks.com/matlabcentral/newsreader/view_thread/249306
					#print "Arbitrary P: $Pvalue \n\n";
					
					
					 #Calculate the observed test statistic, KSobs.
					 #Find all the possible permutation of the data and calculate KS for each permutation.
					 #The p-value is found by
					 #p-value=# of KS≥KSobstotal # of permutations
					 
					 #unreasonable >_>;
				 }
			 }
			 else {
				print "This value was never sampled. \n";
				$parameterschisflag[$pariter] = 0;
			 }
			
		}
	}

	
	
	
}

##?##?## INITIALIZATION FUNCTIONS ##?##?##

# INIT PHASE: After arguments are handled, determine the comment character
sub determineOutputCommentChar {
	#Makes assumptions on the comment character based on type
	#Reporting wont work if not .c or .s...
	if ($outname2 eq ".c") {
		$reportcharacter = "//";
	}
	elsif ($outname2 eq ".s") {
		$reportcharacter = "#";
	}
	else {
		$headerflag = 0;
	}
}
# INIT PHASE: Handle command line arguments
sub handleArguments {
	#First Argument should be either the filename or a -h
	if (defined $ARGV[0]) {
		#If -h arugment
		if (lc($ARGV[0]) eq '-h') {
			print "Usage: ./genesis.pl [name of genesis file] [options]\n\n";
			print "Usage: ./genesis.pl [name of genesis program] [name of template program] [options]\n\n";

			print "  Possible options: \n";
			for(my $i = 0; $i < scalar @commandlinearguments; $i++  ) {
				print "    " . ${$commandlinearguments[$i]}[0];
			
				my $length = length ${$commandlinearguments[$i]}[0];
			
				for (my $j = 0; $j < 20 - $length; $j++) {
					print " ";
				}
				
				if (${$commandlinearguments[$i]}[4] == 0) {
					print " (can be ${$commandlinearguments[$i]}[5])";
				}
				elsif (${$commandlinearguments[$i]}[4] > 1) {
					print " (default: ${$commandlinearguments[$i]}[5])";
				}
				elsif (${$commandlinearguments[$i]}[4] == -1) {
					print " (can be string*string (ex. Gen*.out))";
				}
				print "\n";
			}
			
			print "\n  Example usage:\n ./genesis.pl ./GenesisPrograms/Testcases/spec-demo.c printParsing=2 printGenerate=2\n";
			
			exit;
		}
		#If filename
		elsif ($ARGV[0] ne '') {
			if (! open (GENPROGFILE, "<:crlf", $ARGV[0])) {
				print "Some sort of open error for Genesis program '$ARGV[0]'. Exiting.";
				exit;
			}
			$filename = $ARGV[0];
		}
		#If there is none, open a default. This shouldnt happen actually.
		else {
			if (! open (GENPROGFILE, "<:crlf", './GenesisPrograms/spec-demo.c')) {
				print "Some sort of open error default for demo Genesis program. Exiting.";
				exit;
			}
			$filename = "./GenesisPrograms/spec-demo.c"
		}
	}
	#If there is none, open a default, one of these wont happen...
	else {
		if (! open (GENPROGFILE, "<:crlf", './GenesisPrograms/spec-demo.c')) {
			print "Some sort of open error for default demo Genesis program. Exiting.";
			exit;
		}
		$filename = "./GenesisPrograms/spec-demo.c"
	}
	
	#$i counts through command line arguments.
	#Starts at 1 if there's no target file. Starts at 2 if there is.
	my $i;
	if (!defined $ARGV[1] || (defined $ARGV[1] && $ARGV[1] =~ /^[\s]*(([\w]+)=([^\)]*))(.*)$/)) {
		$filename2 = "";
		$i = 1;
	}
	else {
		#Opens target code file.
		if (! open (TEMPLATEPROGFILE, "<:crlf", $ARGV[1])) {
			print "Some sort of open error for target code file '$ARGV[1]'. Exiting.";
			exit;
		}
		$filename2 = $ARGV[1];
		$i = 2;
	}

	for (; $i < scalar @ARGV; $i++) {
		setcommandlineargs($ARGV[$i]);
	}
	#Once the files involved is known, determine the comment char
	determineOutputCommentChar();
	
	if ($printintroflag != 0) {
		print " Using Genesis Program: $filename!\n";
		if (defined $filename2) {
			print " Using Target Code File: $filename2!\n";
		}
		print " Using Output directory: $outDir!\n";
		print " Using Instance Program format: $outname1*$outname2!\n\n";
	}
}
# INIT PHASE: Open file for outputting info if needed
sub openOutputFiles {	
	if (defined $dataoutfilename) {
		open($dataoutfile, '>', $dataoutfilename) or die;
	}
	else {
		$dataoutfile = \*STDOUT;
	}
}


##?##?## PHASE1: PARSING THE GENESIS PROGRAM ##?##?##

# PARSING PHASE: check if used line is a keyword, and not to be substituted
sub testNameDoubles {
	#Check for double Genesis name duplication (values, vars, etc)
	my $text = $_[0];
	my $infeature = $_[1];
	my $type = $_[2];
	
	my $error = 0;
	my $errorType;
	
	for (my $j = 0; $j < scalar @{$namesforlocality[$parsebracketcounter+1]}; $j++) {
	
		if ($text eq ${$namesforlocality[$parsebracketcounter+1]}[$j]) {
			printerror ("X", "", "$type '$text'", "$type with name '$text' already exists.");
		}
	}
	
	for (my $j = 0; $j < scalar @globalnames; $j++) {
		if ($text eq $globalnames[$j]) {
			printerror ("X2", "", "$type '$text'", "$type with name '$text' already exists.");
		}
	}
	for (my $j = 0; $j < scalar @programnames; $j++) {
		if ($text eq $programnames[$j]) {
			printerror ("X3", "", "$type '$text'", "$type with name '$text' already exists.");
		}
	}

	${$namesforlocality[$parsebracketcounter+1]}[scalar @{$namesforlocality[$parsebracketcounter+1]}] = $text;

}

sub initiateGlobalSection {
	printP (2, ' Global Section! '. "\n");
				
	if ($globalexistsflag == 1) {
		printerror ("CL", "", "global", "More than one global section.");
	}
	
	$globalexistsflag = 1;
	
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
	$parsebracketcounter++;
	my @temp;
	$namesforlocality[$parsebracketcounter+1] = \@temp;
	$brackettype[$parsebracketcounter] = "global";
	
	$currentbracket[$parsebracketcounter] = "global";
	#$currentfeature = "global";
}

sub initiateProgramSection {
	printP (2, ' Program Section! '. "\n");
				
	if ($programexistsflag == 1) {
		printerror ("BM", "", "program", "More than one program section.");
	}
	
	$programexistsflag = 1;
	
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
	$parsebracketcounter++;
	my @temp;
	$namesforlocality[$parsebracketcounter+1] = \@temp;
	$brackettype[$parsebracketcounter] = "program";
	
	$currentbracket[$parsebracketcounter] = "program";
	#$currentfeature = "program";
}

sub initiateFeatureSection {
	my $info = $_[0];
	printP (2, ' Feature! '. "\n");
				
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
	$parsebracketcounter++;
	my @temp;
	$namesforlocality[$parsebracketcounter+1] = \@temp;
	$brackettype[$parsebracketcounter] = "feature";
	
	if ($info =~ /^(([\w]*\([\w]*\)[\s]*)*)([\w]+)[\s]*(\(.*\))?[\s]*$/) {
						
		my $args = $1;
		my $featurename = $3;
		my $samplevar = $4;
		my @params;
		my @parameterlist;
		setfeatureargs($args);
		
		if (defined $samplevar) {
			$samplevar =~ s/^\(|\)$//g;

			@parameterlist = split(",", $samplevar);
			for (my $i = 0; $i < scalar @parameterlist; $i++) {
				$parameterlist[$i] =~ s/^\s+|\s+$//g;
			}
			for(my $i = 0; $i < scalar @parameterlist; $i++) {
				printP (3, "		 Parameter " . $i . ": '" . $parameterlist[$i] . "'\n");
			}
		}
		testNameDoubles ($featurename, "", "Feature");
		$featuresparameterlist[scalar @featuresparameterlist] = \@params;
		$featuresparams[scalar @featuresparams] = \@parameterlist;
		$featuresparamsvalid[scalar @featuresparamsvalid] = 0;
	
		$currentfeature = $featurename;
		if ($featurename eq "program") {
			printerror ("BN", "", $info, "Feature cannot be named program.");

		}
		if ($featurename eq "global") {
			printerror ("CZ", "", $info, "Feature cannot be named global.");

		}
		$features[scalar @features] = $featurename;
		$featuresvalid[scalar @featuresvalid] = 0;
		printP (3, "   Multiline Feature with params! '$currentfeature'\n");
	}
	else {
		printerror ("N", "", $info, "Invalid feature line.");
	}
	$currentbracket[$parsebracketcounter] = $features[scalar @features -1];
	return (1);
}

sub initiateGenerateSection {
	my $info = $_[0];
	printP (2, " Generate! \n");
				
	if ($info =~ /^[\s]*$/) {
		printerror ("BX", "", "Generate line", "No number to generate!");
	}
	
	my $notouch;
	my $multiline = 0;
	my $generatenum;
	my $distributioninfo;
	if ($info =~ /[\w\s]+ with/) {
		($generatenum, $distributioninfo) = split(" with", $info, 2);
		if ($distributioninfo =~ /^[\s]*$/) {
			$multiline = 1;
		}
		else {
			$multiline = 0;
		}
	}
	else {
		$distributioninfo = "";
		$generatenum = $info;
		$multiline = 0;
	}
	($generatenum, $notouch) = split(" ", $generatenum, 2);
	$generates[scalar @generates] = $generatenum;
	if (!defined $notouch) {
		$gentouch[scalar @gentouch] = 1;
	}
	elsif ($notouch eq "notouch") {
		$gentouch[scalar @gentouch] = 0;
	}
	else {
		printerror ("BE", "", "'$notouch'", "Weird argument for generate.");
	}
	if ($multiline == 0) {
		$gendistribute[scalar @gendistribute] = $distributioninfo;
	}
	else {
		my $gentext; #reading from the generate line
		my $genline = "";
		$gentext = <GENPROGFILE>;
		$gentext =~ s/^\s+|\s+$//g;

		while ($gentext ne "end") {
			if ($genline eq "") {
			$genline = $gentext;
			}
			else {
				$genline = $genline.",".$gentext;
			}
			$gentext = <GENPROGFILE>;
			$gentext =~ s/^\s+|\s+$//g;
		}
		$gendistribute[scalar @gendistribute] = $genline;

	}
	printP (3, "   Create $generatenum with '$gendistribute[scalar @gendistribute-1]'\n");
}

sub addToFeature {
	my $text = $_[0];
	
	#Add to current context
	${$currentgens[$parsebracketcounter]}[scalar @{$currentgens[$parsebracketcounter]}] = "$text\n";
	printP (3, "   Add line to feature. Feature right now: \n");
	for (my $funiter = 0; $funiter < scalar @{$currentgens[$parsebracketcounter]}; $funiter++) {
		printP (3, "   Feature line $funiter: ${$currentgens[$parsebracketcounter]}[$funiter]");
	}
	
	#Update parameter list, if we are still in the global section
	if ($brackettype[$parsebracketcounter] eq "global") { 
		#A parameter exists & the last was enumerate
		# and either
		#	- globalenum is empty, or
		#	- the last entry is not the same as the last parameter
		if ((scalar @parametersfullflag > 0 && $parametersfullflag[scalar @parametersfullflag-1] == 1) 
		&& (scalar @globalenum == 0 || (scalar @globalenum > 0 && $globalenum[scalar @globalenum-1] != scalar @{$currentgens[$parsebracketcounter]} -1 ))) {
			$globalenum[scalar @globalenum] = scalar @{$currentgens[$parsebracketcounter]} -1;
		}
		if ($distlineflag == 1) {
			$globaldist[scalar @globaldist] = scalar @{$currentgens[$parsebracketcounter]} -1;
		}
		if ($reportlineflag == 1) {
			$globalreport[scalar @globalreport] = scalar @{$currentgens[$parsebracketcounter]} -1;
		}
	}
	#Update parameter list, if we are still in the program section
	elsif ($brackettype[$parsebracketcounter] eq "program") { 
		#A parameter exists & the last was enumerate
		# and either
		#	- programenum is empty, or
		#	- the last entry is not the same as the last parameter

		if ((scalar @parametersfullflag > 0 && $parametersfullflag[scalar @parametersfullflag-1] == 1) 
		&& (scalar @programenum == 0 || (scalar @programenum > 0 && $programenum[scalar @programenum-1] != scalar @{$currentgens[$parsebracketcounter]} -1 ))) {
			$programenum[scalar @programenum] = scalar @{$currentgens[$parsebracketcounter]} -1;
		}
		if ($distlineflag == 1) {
			$programdist[scalar @programdist] = scalar @{$currentgens[$parsebracketcounter]} -1;
		}
		if ($reportlineflag == 1) {
			$programreport[scalar @programreport] = scalar @{$currentgens[$parsebracketcounter]} -1;
		}
	}
}

# PARSING PHASE: Parses the genesis line and stores the information
sub parseGenesisLine {
	my $text = $_[0];
	my $keyword;
	my $info;
	
	if (!defined $text) {
		printerror ("AC", "", "End of header", "No end genesis line.");
	}
	$linenumber++;
	#$/ = "\r\n";
	chomp($text);					
	
	$reportlineflag = 0;
	$distlineflag = 0;
	
	($keyword, $info) = split(" ", $text, 2);
	
	if ($text =~ /^([\w,\[\]\s]*)[\s]*=[\s]*[$generegex]+(.*)$/) {
		$equalWithoutGenmathFlag = 1;
	}
	
	# If the first word in the line may be a Genesis Construct
	if (defined $keyword) {
	
		#If it is a Genesis comment
		if (lc($keyword) =~ /^\/\/\//) {
			printP (2, ' Genesis Comment!'. "\n");
			#do nothing
			return $text;
		}
		
		# If we are not in a section yet (global, program or feature, or the generate line, or the end genesis line)
		# Else, throw an error/assume it is a comment
		elsif ($parsebracketcounter < 0) {
			# Allows the following on base level when not in a section:
			# - geninclude
			# - global
			# - program
			# - feature
			# - generate
			# - end genesis
			# - any other line may or may not be ignored
			if (lc($keyword) eq "geninclude") {
				initiateGenincludeStatement($info);
				return $text;
			}
			elsif (lc($keyword) eq "global") {
				initiateGlobalSection();
				return $text;
			}
			elsif (lc($keyword) eq "program") {
				initiateProgramSection();
				return $text;
			}
			elsif (lc($keyword) eq "feature") {
				initiateFeatureSection($info);
				return $text;
			}
			#By design, this is in the bracket < 0 condition, meaning outside of features. Maybe change this later by design.
			elsif (lc($keyword) eq "generate") {
				initiateGenerateSection($info);
				return $text;
			}
			elsif (lc($keyword) eq "end" && defined $info && lc($info) eq "genesis") {
				printP (2, "End genesis! \n");
				$checkoneheaderflag = 1;
				return "";
			}
			else {
				#If flag is off, line is considered an error.
				#If flag is on, line is considered a comment.
				if ($headercommentsflag == 0) {
					printerror ("CK", "", "$text" , "A line in the header is outside the global/program/features section.");
				}
				else {
					printP (2, "Assuming comments! \n");
					return "";
				}
			}
		}
		
		# Allows the following if we are in a section 
		# - value
		# - varlist
		# - stored feature
		# - variable
		# - add
		# - remove
		# - genif
		# - genloop
		# - distribution
		# - genmath
		# - genif
		# - genloop
		# - any code snippet
		# (generate is an error)
		# (end genesis is an error)
		# - end
		elsif ($parsebracketcounter >= 0) {
		
			# Remove leading spaces
			for(my $i = -1; $i <= $parsebracketcounter; $i++) {
				$text =~ s/^(\s)//;
			}
		
			if ($text =~ /^[\s]*end[\s]*genesis[\s]*$/) {
				printerror ("AB", "", "end genesis", "Missing 'end' statement.");
			}
			elsif (lc($keyword) eq "generate") {
				printerror ("AE", "", "generate line", "Generate line inside a feature '$currentfeature', incorrect usage.");
			}
			elsif (lc($keyword) eq "value") {
				return parsevalue($info,$text);
			}
			
			elsif (lc($keyword) eq "varlist") {
				return parsevarlist($info,$text);
			}

			elsif (lc($keyword) eq "variable") {
				return parsevariable($info,$text);
			}
						
			elsif (lc($keyword) eq "feature") {
				return parsestored($info,$text);
			}
			
			elsif (lc($keyword) eq "add") {
				return parseadd($info,$text);
			}
			
			elsif (lc($keyword) eq "remove") {
				return parseremove($info,$text);
			}
			
			elsif (lc($keyword) eq "distribution") {
				return parsedistribution($info,$text);			
			}
			elsif (lc($keyword) eq "genmath") {
				return parsegenmath($info,$text);	
			}
			
			elsif (lc($keyword) eq "genif" || lc($keyword) eq "genelsif" || lc($keyword) eq "genelse") {
				return parsegenif($info, $text, $keyword);
			}
			
			elsif ($text =~ /^[\s]*genloop[\s]*(.*)/) {
				return parsegenloop($info, $text);
			}			
			
			elsif ($text =~ /^[\s]*end[\s]*$/) {
				return parseend ($info, $text);
			}
			else {
				printP (2, " Actual line snippet.\n");
				if ($brackettype[0] eq "global") {
					printwarning ("WK", "", $text, "Code snippet in global section will not be used.");
				}
				
				if ($brackettype[0] eq "program") {
					printwarning ("WL", "", $text, "Code snippet in program section will not be used.");
				}
				
				addToFeature($text);
				
				if ($currentfeature ne "") {
					$samplewarningflag = 0;
				}
				return $text;
			}
		}
		else {
			printerror ("ZZA", "", "$text" , "Something is off with the compiler. Tell Alton.");
		}
		printerror ("ZZB", "", "$text" , "Something is off with the compiler. Tell Alton.");
	}
	#Blank line with no keyword
	else {
		printP (2, " Blank line!\n");
		return $text;
	}
}

sub storeGenif {
	my $type = $_[0];
	my $listlocation = $_[1];
	if ($currentbracket[$parsebracketcounter] =~ /^([$refqregex]+) ([\d]*)[\s]*$/) {
		$genifinequality[scalar @genifinequality] = $1;
		$genifid[scalar @genifid]  = $2;
		$geniffeature[scalar @geniffeature]  = $currentfeature;
		$geniflist[scalar @geniflist] = $listlocation;
		$geniftype[scalar @geniftype] = $type;
		printP (3, "  Var: '" . $1. "'\n");
		printP (3, "  ID: " ."'" . $2 ."'". "\n");
	}
	elsif ($type == 0) {
		printerror ("AW", "", "$currentbracket[$parsebracketcounter]", "Bad genif condition.");
	}
	elsif ($type == 1) {
		printerror ("AX", "", "$currentbracket[$parsebracketcounter]", "Bad genelsif condition.");
	}
	else {
		printerror ("ZZC", "", "storeGenif", "Something is off with the compiler. Tell Alton.");
	}
									
}


# PARSING PHASE: Open geninclude and parse file
sub initiateGenincludeStatement {
	my $filename = $_[0];
	$libfilename = "./LibraryFiles/$filename"; 
	printP (2, ' Geninclude Statement! '. "\n");
	if ($libfilename ne '') {	
		if (! open (LIBRARYFILE, "<:crlf", $libfilename)) {
			print "Some sort of open error for library file '$libfilename'. Exiting.";
			exit;
		}
	}
	else {
		if (! open (LIBRARYFILE, "<:crlf", './LibraryFiles/varlist_c.lib')) {
			print "Some sort of open error for default library file 'varlist_c.lib'. Exiting.";
			exit;
		}
	}
	
	while (my $text = <LIBRARYFILE>) {
		#print "TEXT: '$text'\n";
		
		parseGenesisLine($text);
	}
	
	close(LIBRARYFILE);
}
# PARSING PHASE: Parse and store a value
sub parsevalue {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' Value!'. "\n");
	if ($currentfeature ne "") {
		$samplewarningflag = 1;
	}
	if (defined $info) {
		my @valuelist = split(";", $info);
		
		my $bracketflag = 0;
		$noreplacementcounter = 0;
	
		# for every semicolon split
		for(my $priter = 0; $priter < scalar @valuelist; $priter++) {
			my $search = "";
			$noreplacementcounter++;

			$valuelist[$priter] =~ s/^\s+|\s+$//g;
			
			$search = $valuelist[$priter];

			$bracketflag++ while ($valuelist[$priter] =~ /\{/g);
			$bracketflag-- while ($valuelist[$priter] =~ /\}/g);
			

			while ($bracketflag >= 1) {
				$priter++;
				$search = $search . ";" . $valuelist[$priter];
				$bracketflag++ while ($valuelist[$priter] =~ /\{/g);
				$bracketflag-- while ($valuelist[$priter] =~ /\}/g);
			}
					
			my $type = 0;
			my @parameter;
			my $range;
			my $args; 
			if ($search =~ /^([\w,\[\$\{\}\]]*)$/) {
				$type = 1;
				@parameter = split(",", $1);
				$args = "";
			}
			elsif ($search =~ /^([\w,\[\$\{\}\]\s]*)[\s]+sample[\s]+([$equaregex]+)(.*)$/) {
				$type = 2;
				@parameter = split(",", $1);
				$range = $2;
				$args = $3;
			}
			elsif ($search =~ /^([\w,\[\$\{\}\]\s]*)[\s]+sample[\s]+({[-$generegex,\.:;\s]*})(.*)$/) {
				$type = 3;
				@parameter = split(",", $1);
				my $tempdistname = "_a" . scalar @localdistributions;
				$range = $tempdistname;
				$localdistributions[scalar @localdistributions] = $tempdistname . " = " . $2;
				$args = $3;
			}
			elsif ($search =~ /^([\w,\[\$\{\}\]\s]*)[\s]+enumerate[\s]+([$equaregex]*)(.*)$/) {
				#TODO: Enumerate not allowed in features for now
				if ($currentfeature ne "" && $currentfeature ne "program") {
					printerror ("AL", "", "Value $1 with range $2", "Enumerate is invalid while in a feature due to possible infinite nesting. Please leave enumerate outside a feature.");
				}
				$type = 4;
				@parameter = split(",", $1);
				$range = $2;
				$args = $3;
			}
			elsif ($search =~ /^([\w,\[\]\$\{\}\s]*)[\s]*=[\s]*([\'|\"]?[$generegex]+[\'|\"]?)(.*)$/) {
				$type = 5;
				@parameter = split(",", $1);
				$range = $2;
				$args = $3;
			
			}
			#Old method where from is used instead of sample
			elsif($search =~ /^([\w,\[\]\s]*)[\s]+from[\s]+([$equaregex]+)(.*)$/ || $search =~ /^([\w,\[\]\s]*)[\s]+from[\s]+{[-$generegex,:;\s]*}(.*)$/ ) {
				printerror ("BS", "", $text, "Invalid value line. (Maybe change 'from' to 'sample'?)");
			}
			#Else bad error
			else {
				printerror ("A", "", $text, "Invalid value line.");
			}			
			#for every value split
			for(my $pariter = 0; $pariter < scalar @parameter; $pariter++) {
				my $bracketnum;
				my $arrayflag;
				#check if it is a value array
				if ($parameter[$pariter] =~ /^([\w]*)\[([$referegex]*)\]/ ) {
					$bracketnum = $2;
					$parameter[$pariter] = $1;
					$arrayflag = 1;
					if ($bracketnum eq "") {
						printerror ("Q", "", "Value $parameter[$pariter]", "Nothing in the brackets for value array.");
					}
				}
				# else, not an array
				else {
					$arrayflag = 0;
					$bracketnum = -1;
				}
			
				# While cycling through the array (or if it is not an array)
				if ($type==1) {
					$parametersevalflag[scalar @parametersevalflag] = 0;
					$parametersfullflag[scalar @parametersfullflag] = 0;
				}
				
				# Value sampling
				elsif ($type==2) {
					$parametersevalflag[scalar @parametersevalflag] = 1;
					$parametersfullflag[scalar @parametersfullflag] = 0;
				}
				#Value sampling with in-line distributions
				elsif ($type==3) {
					$parametersevalflag[scalar @parametersevalflag] = 1;
					$parametersfullflag[scalar @parametersfullflag] = 0;
				}
				#Value enumerate
				elsif ($type==4) {
				
					$numtoenumerate = 1;
					$parametersevalflag[scalar @parametersevalflag] = 1;
					$parametersfullflag[scalar @parametersfullflag] = 1;
				}
				#Value equals
				elsif ($type==5) {
					$parametersevalflag[scalar @parametersevalflag] = 0;
					$parametersfullflag[scalar @parametersfullflag] = 0;
				}
				#Shouldnt happen, captured by error A. Incase.
				else {
					printerror ("ZZD", "", "'$search'", "Something is off with the compiler. Tell Alton.");
				}
				$parameter[$pariter] =~ s/^\s+|\s+$//g;
				setvalueargs($args);
				if (!defined $range) {
					$parametersdistvar[scalar @parametersdistvar] = "";
					$parametersequalpar[scalar @parametersequalpar] = "";
				}
				else {
					$range =~ s/^\s*|\s*$//g;
					if ($parametersevalflag[scalar @parametersevalflag -1] == 1) {
						$parametersdistvar[scalar @parametersdistvar] = $range;
						$parametersequalpar[scalar @parametersequalpar] = "";
					}
					else {
						$parametersdistvar[scalar @parametersdistvar] = "";
						$parametersequalpar[scalar @parametersequalpar] = $range;
					}
				}
				testNameDoubles ($parameter[$pariter], $currentfeature, "Value");
				$parameters[scalar @parameters] = $parameter[$pariter];
				
				if ($arrayflag == 1) {
					$parametersarrayflag[scalar @parametersarrayflag] = 1;	
					$parametersarraybrackets[scalar @parametersarraybrackets] = $bracketnum;
				}
				else {
					$parametersarrayflag[scalar @parametersarrayflag] = 0;
					$parametersarraybrackets[scalar @parametersarraybrackets] = "";
				}
				
				if ($brackettype[0] eq "global") {
					$parametersglobalflag[scalar @parametersglobalflag] = 1;
				}
				else {
					$parametersglobalflag[scalar @parametersglobalflag] = 0;
				}
				
				$parametersfeature[scalar @parametersfeature] = $currentfeature;
				$parametersrealflag[scalar @parametersrealflag] = 0;
				#$parameterslocalcounter[scalar @parameterslocalcounter] = 0;
				#$parametersstartcounter[scalar @parametersstartcounter] = 0;
				$parametersglobalcounter[scalar @parametersglobalcounter] = 0;
				$parametersnumber[scalar @parametersnumber] = $valuecounter;
				
				printP (3, "   Value " . (scalar @parameters- 1) . ": '" . $parameters[scalar @parameters- 1] . "' from '" . $parametersdistvar[scalar @parameters- 1] . "'\n");
					
			}
			
		}
	}
	else {
		printerror ("BY", "", $text, "Blank value line.");
	}
	#increase counter and return value
	$valuecounter++;
	my $tempvalue = $valuecounter-1;
	my $returnvalue = "value $tempvalue";
	
	addToFeature($returnvalue);
	return $returnvalue;
}
# PARSING PHASE: Parse and store a varlist
sub parsevarlist {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' Varlist!'. "\n");
			
	if ($currentfeature ne "") {
		$samplewarningflag = 2;
	}
						

	if (defined $info && $info =~ /^([\w]*)[\s]*\[[\s]*([$referegex]*)\](.*)[\s]*$/) {
		$varlistevalflag[scalar @varlistevalflag] = 1;						
		$varlistname[scalar @varlistname] = $1;
		$varlistarg[scalar @varlistarg] = $2;
		$varlistequalvar[scalar @varlistequalvar] = "";
		$varlistvalidity[scalar @varlistvalidity] = -1;
		setvarlistargs($3);
	}
	#Varlist with from
	
	elsif (defined $info && $info =~ /^([\w]*)[\s]*from[\s]*([$equaregex]*)(.*)[\s]*$/) {
		$varlistevalflag[scalar @varlistevalflag] = 0;					
		$varlistname[scalar @varlistname] = $1;
		$varlistarg[scalar @varlistarg] = "";
		$varlistequalvar[scalar @varlistequalvar] = $2;
		$varlistvalidity[scalar @varlistvalidity] = 0;
		if ($3 =~ /[\S]/) {
			printerror ("BD", "", $text, "Varlists using 'from' should not have any arguments.");
		}
		setvarlistargs("");
	}
	else {
		printerror ("C", "", $text, "Invalid varlist line.");
	}
	$varlistcounter++;
	my $tempvalue = $varlistcounter-1;
	my $returnvalue = "varlist $tempvalue";
	
	addToFeature($returnvalue);
	return $returnvalue;
}
# PARSING PHASE: Parse and store a variable
sub parsevariable {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' Variable!'. "\n");
			
	if ($currentfeature ne "") {
		$samplewarningflag = 3;
	}
	
	if (defined $info) {
		my @variable = split(";", $info);
		# for every semicolon split
		for(my $variter = 0; $variter < scalar @variable; $variter++) {
			my @parameter;
			my $range;
			my $args;
			my $type;
			if ($variable[$variter] =~ /^([\w,\s]*)[\s]+from[\s]+([$referegex]+)[\s]*(.*)$/) {
				@parameter = split(",", $1);
				$range = $2;
				$args = $3;
				$type = 1;
				$range =~ s/^\s*|\s*$//g;
			}
			elsif ($variable[$variter] =~ /^([\w,\s]*)[\s]*=[\s]*([$generegex]+)[\s]*(.*)$/) {
				@parameter = split(",", $1);
				$range = $2;
				$args = $3;
				$type = 2;
				$range =~ s/^\s*|\s*$//g;
			}
			else {
				printerror ("D", "", $text, "Invalid variable line.");
			}
			# for every parameter split
			for(my $pariter = 0; $pariter < scalar @parameter; $pariter++) {
				$parameter[$pariter] =~ s/^\s+|\s+$//g;
				if ($type == 1) {
					my $tempargs = $args;
					$variablesevalflag[scalar @variablesevalflag] = 1;
					setvarargs($tempargs);
				}
				elsif($type == 2) {
					my $tempargs = $args;
					$variablesevalflag[scalar @variablesevalflag] = 0;
					setvarargs($args);
				}
				
				testNameDoubles ($parameter[$pariter], $currentfeature, "Var");
				
				$variables[scalar @variables] = $parameter[$pariter];
				$variablesfeature[scalar @variablesfeature] = $currentfeature;
				
				#Sampling
				if ($variablesevalflag[scalar @variablesevalflag -1] == 1) {
					$variablesvarlistvar[scalar @variablesvarlistvar] = $range;
					$variablesequalpar[scalar @variablesequalpar] = $range;
				}
				#Equals
				else {
					$variablesvarlistvar[scalar @variablesvarlistvar] = "";
					
					for(my $variter2 = 0; $variter2 < scalar @variables; $variter2++) {
						if ($range =~ /\$\{$variables[$variter2]\}/) {
							$variablesvarlistvar[scalar @variablesvarlistvar-1] = $variablesvarlistvar[$variter2];
						}
					}
					
					if ($variablesvarlistvar[scalar @variablesvarlistvar-1] eq "") {
						printerror ("BT", "", "$range" , "Not a valid varlist target for a variable.");
					}
					
					$variablesequalpar[scalar @variablesequalpar] = $range;
				}
				
				#Global Flag
				if ($parsebracketcounter == -1) {
					$variablesglobalflag[scalar @variablesglobalflag] = 1;
				}
				else {
					$variablesglobalflag[scalar @variablesglobalflag] = 0;
				}
				
				$variablesnumber[scalar @variablesnumber] = $variablecounter;
	
				printP (3, "  Variable " . (scalar @variables- 1) . ": '". $variables[scalar @variables- 1]. "' from " . $variablesvarlistvar[scalar @variables- 1] . "\n");	
			}

		}
		
	}
	else {
		printerror ("AT", "", $text, "Blank variable line.");
	}
	$variablecounter++;
	my $tempvalue = $variablecounter-1;
	my $returnvalue = "variable $tempvalue";
	
	addToFeature($returnvalue);
	return $returnvalue;
}
# PARSING PHASE: Parse and store a feature instance
sub parsestored {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' Stored!'. "\n");
	
	#
	if ($currentfeature ne "") {
		$samplewarningflag = 3;
	}
	if (defined $info) {
		my @storedline = split(";", $info);
		# for every semicolon split
		for(my $variter = 0; $variter < scalar @storedline; $variter++) {
			my @parameter;
			my $range;
			my $args;
			if ($storedline[$variter] =~ /^([\w,\s]*)[\s]+process[\s]+([$referegex]*)[\s]*(.*)$/) {
				@parameter = split(",", $1);
				$range = $2;
				$args = $3;
				$range =~ s/^\s*|\s*$//g;
				# for every feature name split
			}
			else {
				printerror ("CN", "", $text, "Invalid stored line.");
			}
			for(my $pariter = 0; $pariter < scalar @parameter; $pariter++) {
				$parameter[$pariter] =~ s/^\s+|\s+$//g;
				
				testNameDoubles ($parameter[$pariter], $currentfeature, "Stored");
				
				$stored[scalar @stored] = $parameter[$pariter];
				$storedvar[scalar @storedvar] = $range;
				$storedfeature[scalar @storedfeature] = $currentfeature;
				if ($parsebracketcounter == -1) {
					$storedglobalflag[scalar @storedglobalflag] = 1;
				}
				else {
					$storedglobalflag[scalar @storedglobalflag] = 0;
				}
				
				$storednumber[scalar @storednumber] = $storedcounter;
	
				printP (3, "  Stored " . (scalar @stored- 1) . ": '". $stored[scalar @stored- 1]. "'\n");	
			}
		}
	}
	else {
		printerror ("CI", "", $text, "Blank stored line.");
	}
	$storedcounter++;
	my $tempvalue = $storedcounter-1;
	my $returnvalue = "stored $tempvalue";
	
	addToFeature($returnvalue);
	return $returnvalue;
}
# PARSING PHASE: Parse and store a add line
sub parseadd {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' AddVariable!'. "\n");
	
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
	if (defined $info) {
		my @valuelist = split(";", $info);
		# for every semicolon split
		for(my $priter = 0; $priter < scalar @valuelist; $priter++) {
		$valuelist[$priter] =~ s/^\s+|\s+$//g;
			my $samplevar;
			my $range;
			if ($valuelist[$priter] =~ /^([\w,\s]*)[\s]+to[\s]+([$referegex]+)[\s]*$/) {
				$samplevar = $1;
				$range = $2;
				$samplevar =~ s/^\s+|\s+$//g;
				$range =~ s/^\s+|\s+$//g;
			}
			else {
				if ($valuelist[$priter] =~ /^([\w,\s]*)[\s]+to[\s]+varlist[\s]+([$referegex]+)[\s]*$/) {
					printerror ("E1", "", $text, "Invalid add line. HINT: varlist keyword is not needed anymore.");
				}
				else {
					printerror ("E", "", $text, "Invalid add line.");
				}
			}
			my @addvariable = split(",", $samplevar);
			# for every Genesis name split
			for(my $variter = 0; $variter < scalar @addvariable; $variter++) {
				$addvariable[$variter] =~ s/^\s+|\s+$//g;
				$addvariables[scalar @addvariables] = $addvariable[$variter];
				$addvariablesfeature[scalar @addvariablesfeature] = $currentfeature;
				$addvariablesvarlistvar[scalar @addvariablesvarlistvar] = $range;
				$addvariablesnumber[scalar @addvariablesnumber] = $addcounter;
				printP (3, "  AddVariable " . (scalar @addvariables- 1) . ": '". $addvariables[scalar @addvariables- 1]. "' to " . $addvariablesvarlistvar[scalar @addvariables- 1] . "\n");	
			}
		}
	}
	else {
		printerror ("E", "", $text, "Invalid addvar line.");
	}
	$addcounter++;
	my $tempvalue = $addcounter-1;
	my $returnvalue = "add $tempvalue";
	
	addToFeature($returnvalue);
	return $returnvalue;
}
# PARSING PHASE: Parse and store a remove line
sub parseremove {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' RemVariable!'. "\n");
			
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
	if (defined $info) {
	
		my @valuelist = split(";", $info);
		
		# for every semicolon split
		for(my $priter = 0; $priter < scalar @valuelist; $priter++) {
		$valuelist[$priter] =~ s/^\s+|\s+$//g;
			my $samplevar;
			my $range;
			if ($valuelist[$priter] =~ /^([\w,\s]*)[\s]+from[\s]+([$referegex]+)[\s]*$/) {
				$samplevar = $1;
				$range = $2;
				$samplevar =~ s/^\s+|\s+$//g;
				$range =~ s/^\s+|\s+$//g;
			}
			else {
				if ($valuelist[$priter] =~ /^([\w,\s]*)[\s]+from[\s]+varlist[\s]+([$referegex]+)[\s]*$/) {
					printerror ("F1", "", $text, "Invalid rem line. HINT: varlist keyword is not needed anymore.");
				}
				else {
					printerror ("F", "", $text, "Invalid rem line.");
				}
			}
			my @remvariable = split(",", $samplevar);
			# for every Genesis name split
			for(my $variter = 0; $variter < scalar @remvariable; $variter++) {
				$remvariable[$variter] =~ s/^\s+|\s+$//g;
				$remvariables[scalar @remvariables] = $remvariable[$variter];
				$remvariablesfeature[scalar @remvariablesfeature] = $currentfeature;
				$remvariablesvarlistvar[scalar @remvariablesvarlistvar] = $range;
				$remvariablesnumber[scalar @remvariablesnumber] = $remcounter;
				printP (3, "  remvariable " . (scalar @remvariables- 1) . ": '". $remvariables[scalar @remvariables- 1]. "' to " . $remvariablesvarlistvar[scalar @remvariables- 1] . "\n");	
			}
		}
	}
	else {
		printerror ("F", "", $text, "Invalid remvar line.");
	}
	$remcounter++;
	my $tempvalue = $remcounter-1;
	my $returnvalue = "remove $tempvalue";
	
	addToFeature($returnvalue);
	return $returnvalue;
}

sub parsedistribution {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, " Distribution!\n");
	
	if ($currentfeature ne "") {
		$samplewarningflag = 4;
	}

	$distlineflag = 1;
	$globaldistributions[scalar @globaldistributions] = $info;
	my $returntext = "distribution ". scalar @globaldistributions-1;
	addToFeature($returntext);
	return $returntext;
}

sub parsegenmath {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, " Genmath!\n");
	if ($info =~ /^([$referegex,\s]*)[\s]+sample[\s]+([$equaregex]+)(.*)$/ || $info =~ /^([$referegex,\s]*)[\s]+sample[\s]+{[-$generegex,:;\s]*}(.*)$/ ) {
		$distlineflag = 1;
		$genmathdistvar[scalar @genmathdistvar] = $2;
	}
	addToFeature($text);
	return $text;
}

sub parsegenif {
	my $info = $_[0];
	my $text = $_[1];
	my $keyword = $_[2];
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
	my $iftype = 0;
	my $bracket = $parsebracketcounter;
	if (lc($keyword) eq "genif") {
		printP (2, ' Genif! '. "\n");
		$iftype = 1;
		printP (3, " Add genif to feature. Feature right now: \n");
		if (!defined $info || $info =~ /^[\s]*$/) {
			printerror ("CX", "", "$text", "Genif with no arguments!");
		}
	}
	elsif (lc($keyword) eq "genelsif") {
		printP (2, ' Genelsif! '. "\n");
		$iftype = 2;
		printP (3, " Add genelsif to feature. Feature right now: \n");
		if (!defined $info || $info =~ /^[\s]*$/) {
			printerror ("CY", "", "$text", "Genelse with no arguments!");
		}
	}
	elsif (lc($keyword) eq "genelse") {
		printP (2, ' Genelse! '. "\n");
		$iftype = 3;
		printP (3, " Add genelse to feature. Feature right now: \n");
		if (defined $info && $info =~ /[^\s]/) {
			printerror ("AY", "", "$text", "Genelse should not have a condition.");
		}
		$info = "1";
	}
	else {
		printerror ("ZZE", "", "'$text'", "Something is off with the compiler. Tell Alton.");
	}
	
	if ($brackettype[$parsebracketcounter] ne "genelsif" && $brackettype[$parsebracketcounter] ne "genif") {
		if ($iftype == 2) {
			printerror ("AJ", "", "genelsif", "Genelsif without genif");
		}
		elsif ($iftype == 3) {
			printerror ("AK", "", "genelse", "Genelse without genif");
		}
	}
	
	if ($iftype == 2 || $iftype == 3) {
		
		$bracket = $bracket - 1;

		my @tempfunction;
		for (my $funiter = 0; $funiter < scalar @{$currentgens[$parsebracketcounter]}; $funiter++) {
			$tempfunction[scalar @tempfunction] = ${$currentgens[$parsebracketcounter]}[$funiter];
			printP (3, "Feature line $funiter: '${$currentgens[$parsebracketcounter]}[$funiter]'\n");
		}
		
		@{$currentgens[$parsebracketcounter]}=(); 

		
		if ($brackettype[$parsebracketcounter] eq "genif") {
			printP (3, "  Genif name: '" . $currentbracket[$parsebracketcounter]. "'\n");
			storeGenif(0, \@tempfunction);
		}
		
		elsif ($brackettype[$parsebracketcounter] eq "genelsif") {
			printP (3, "  Genelsif name: '" . $currentbracket[$parsebracketcounter]. "'\n");
			storeGenif(1, \@tempfunction);
		}
		if ($iftype == 2) {
			$brackettype[$parsebracketcounter] = "genelsif";
		}
		if ($iftype == 3) {
			$brackettype[$parsebracketcounter] = "genelse";
		}
	}
	elsif ($iftype == 1) {
		$parsebracketcounter++;
		$brackettype[$parsebracketcounter] = "genif";
	}
				
	my @temp;
	$namesforlocality[$parsebracketcounter+1] = \@temp;
	$currentbracket[$parsebracketcounter] = "$info $genifcounter";		
	${$currentgens[$bracket]}[scalar @{$currentgens[$bracket]}] = "genif $genifcounter\n";
	for (my $funiter = 0; $funiter < scalar @{$currentgens[$bracket]}; $funiter++) {
		printP (3, "   Feature line $funiter: ${$currentgens[$bracket]}[$funiter]");
	}
	$genifcounter++;
	return $text;
}

sub parsegenloop {
	my $info = $_[0];
	my $text = $_[1];
	printP (2, ' Genloop! '. "\n");
	if ($currentfeature ne "") {
		$samplewarningflag = 0;
	}
		
	if (!defined $info || $info =~ /^[\s]*$/) {
		printerror ("BZ", "", "$text", "Genloop with no arguments!");
	}
	elsif ($info =~ /^([\w]+[\s]*:[\s]*[$generegex]+[\s]*:[\s]*[$generegex]+[\s]*(:[\s]*[$generegex]+)?)/){
		$brackettype[$parsebracketcounter+1] = "genloop1";
		$info =~ s/\:\s+|\s+\:/\:/g;
		
	}
	elsif ($info =~ /^([$refqregex]+)/){
		$brackettype[$parsebracketcounter+1] = "genloop2";
	}
	else {
		printerror ("BZ", "", "$text", "Genloop with no arguments!");
	}
	
	${$currentgens[$parsebracketcounter]}[scalar @{$currentgens[$parsebracketcounter]}] = "genloop $info ". $genloopcounter ."\n";
	
	printP (3, " Add genloop to feature. Feature right now: \n");
	for (my $funiter = 0; $funiter < scalar @{$currentgens[$parsebracketcounter]}; $funiter++) {
		printP (3, "   Feature line $funiter: ${$currentgens[$parsebracketcounter]}[$funiter]");
	}
	$parsebracketcounter++;
	my @temp;
	$namesforlocality[$parsebracketcounter+1] = \@temp;
	$currentbracket[$parsebracketcounter] = $info . " " . $genloopcounter;
	$genloopcounter++;
	return $text;
}

sub parseend {
	my $info = $_[0];
	my $text = $_[1];
	#The end of something
	$reportlineflag = 0;
	
	#${$currentgens[$parsebracketcounter]}[(scalar @{$currentgens[$parsebracketcounter]})-1] =~ s/\n$//;
	my @tempfunction;
	if (defined $currentgens[$parsebracketcounter]) {
		for (my $funiter = 0; $funiter < scalar @{$currentgens[$parsebracketcounter]}; $funiter++) {
			$tempfunction[scalar @tempfunction] = ${$currentgens[$parsebracketcounter]}[$funiter];
		}
	}
	
	#End of genloop
	if ($brackettype[$parsebracketcounter] eq "genloop1") {
		printP (2, " End Genloop!\n");
		printP (3, "  Genloop1 name: '" . $currentbracket[$parsebracketcounter]. "'\n");
		my $counter;
		my $id;
		my @tempvalue;
		my $varname;
		my $varstart;
		my $varend;
		my $varstride;
						
		($counter, $id) = split(" ", $currentbracket[$parsebracketcounter], 2);
		($varname, $varstart, $varend, $varstride) = split(":", $counter, 4);
		if (!defined $varstride) {
			$varstride = 1;
		}
		
		$varname =~ s/^\s+|\s+$//g;
		$varstart =~ s/^\s+|\s+$//g;
		$varend =~ s/^\s+|\s+$//g;
		$varstride =~ s/^\s+|\s+$//g;
		
		$genloopvar[scalar @genloopvar] = $varname;
		$genloopstart[scalar @genloopstart]  = $varstart;
		$genloopend[scalar @genloopend]  = $varend;
		$genloopstride[scalar @genloopstride]  = $varstride;
		$genloopinequality[scalar@genloopinequality] = "";
		$genloopid[scalar @genloopid]  = $id;
		$genlooplist[scalar @genlooplist]  = \@tempfunction;
		$genloopvalid[scalar @genloopvalid]  = 0;
		$genloopvalue[scalar @genloopvalue]  = \@tempvalue;
		$genloopfeature[scalar @genloopfeature]  = $currentfeature;
		printP (3, "  Var: '" . $varname. "'\n");
		printP (3, "  Var start: " ."'" . $varstart ."'". "\n");
		printP (3, "  Var end: " ."'" . $varend ."'". "\n");
		printP (3, "  Var stride: " ."'" . $varstride ."'". "\n");
	}
	#End of conditional genloop
	elsif ($brackettype[$parsebracketcounter] eq "genloop2") {
		printP (2, " End Genloop!\n");
		printP (3, "  Genloop2 name: '" . $currentbracket[$parsebracketcounter]. "'\n");
		my $counter;
		my $id;
		($counter, $id) = split(" ", $currentbracket[$parsebracketcounter], 2);
		$genloopvar[scalar @genloopvar] = "";
		$genloopstart[scalar @genloopstart]  = "";
		$genloopend[scalar @genloopend]  = "";
		$genloopstride[scalar @genloopstride]  = "";
		$genloopinequality[scalar@genloopinequality] = $counter;
		$genloopid[scalar @genloopid]  = $id;
		$genlooplist[scalar @genlooplist]  = \@tempfunction;
		$genloopvalid[scalar @genloopvalid]  = 0;
		$genloopvalue[scalar @genloopvalue]  = 0;
		$genloopfeature[scalar @genloopfeature]  = $currentfeature;
	}
	#End of genif
	elsif ($brackettype[$parsebracketcounter] eq "genif") {
		printP (2, " End Genif!\n");
		printP (3, "  Genif name: '" . $currentbracket[$parsebracketcounter]. "'\n");
		storeGenif(0, \@tempfunction);

	}
	#End of genelsif
	elsif ($brackettype[$parsebracketcounter] eq "genelsif") {
		printP (2, " End Genelsif!\n");
		printP (3, "  Genelsif name: '" . $currentbracket[$parsebracketcounter]. "'\n");
		storeGenif(1, \@tempfunction);

	}
	#End of genelse
	elsif ($brackettype[$parsebracketcounter] eq "genelse") {
		printP (2, " End Genelse!\n");
		printP (3, "  Genelse name: '" . $currentbracket[$parsebracketcounter]. "'\n");
		storeGenif(2, \@tempfunction);
	}
	#End of feature
	elsif ($brackettype[$parsebracketcounter] eq "feature") {
	
		if ($samplewarningflag == 1) {
			printwarning ("WB", "", "Value", "Done at end of feature?");
		}
		if ($samplewarningflag == 2) {
			printwarning ("WC", "", "Varlist", "Done at end of feature?");
		}
		if ($samplewarningflag ==  3) {
			printwarning ("WD", "", "Variable", "Done at end of feature?");
		}
		if ($samplewarningflag == 4) {
			printwarning ("WE", "", "Distribution", "Done at end of feature?");
		}
		printP (2, " End Feature!\n");
		my $numberoffeats = scalar @featureslist;
		printP (3, "   Feature $numberoffeats: '" . $currentbracket[$parsebracketcounter]. "'\n");
		$featureslist[scalar @featureslist]  = \@tempfunction;
		$currentfeature = "";
	}
	#End of program section
	elsif ($brackettype[$parsebracketcounter] eq "program") {
		printP (2, " End Program Section!\n");
		for (my $funiter = 0; $funiter < scalar @tempfunction; $funiter++) {
			$programcodelines[$funiter]  = $tempfunction[$funiter];
		}
		
		for (my $j = 0; $j < scalar @{$namesforlocality[$parsebracketcounter+1]}; $j++) {
			$programnames[$j] = ${$namesforlocality[$parsebracketcounter+1]}[$j];
		}
		$currentfeature = "";
	}
	#End of global section
	elsif ($brackettype[$parsebracketcounter] eq "global") {
		printP (2, " End Global Section!\n");
		for (my $funiter = 0; $funiter < scalar @tempfunction; $funiter++) {
			$globalcodelines[$funiter]  = $tempfunction[$funiter];
		}
		
		for (my $j = 0; $j < scalar @{$namesforlocality[$parsebracketcounter+1]}; $j++) {
			$globalnames[$j] = ${$namesforlocality[$parsebracketcounter+1]}[$j];
		}
		$currentfeature = "";
	}
	else {
		printerror ("ZZF", "", "'$text'", "Something is off with the compiler. Tell Alton.");
	}
	@{$currentgens[$parsebracketcounter]}=(); 
	$parsebracketcounter--; 
	return $text;
}
	
# PARSING PHASE: Takes in a line, parses and processes all command line args
sub setcommandlineargs {
	my $text = $_[0];
	while ($text =~ /^[\s]*(([\w]+)=([^\)]*))(.*)$/) {
		my $full = $1;
		my $type = $2;
		my $arg = $3;
		my $rest = $4;
		
		my $implemented = 0;
		for (my $i = 0; $i < scalar @commandlinearguments; $i++) {
			if ($type eq ${$commandlinearguments[$i]}[0]) {
				#Check Duplicates
				if (${$commandlinearguments[$i]}[1] == 1) {
					printerror (${$commandlinearguments[$i]}[2], $text, "${$commandlinearguments[$i]}[0] argument more than once.");
				}
				${$commandlinearguments[$i]}[1] = 1;
				#If there are possible values
				if (${$commandlinearguments[$i]}[4] > 0) {
					for (my $j = 1; $j <= ${$commandlinearguments[$i]}[4]; $j++) {
						if ($arg eq ${$commandlinearguments[$i]}[4+$j]) {
							$commandlinechange{$type}($arg);
							$implemented = 1;
						}		
					}
				}
				#Any string format
				elsif (${$commandlinearguments[$i]}[4] == 0) {
					if ($arg) {
						$commandlinechange{$type}($arg);
						$implemented = 1;
					} 						
				}
				# *.* format
				elsif (${$commandlinearguments[$i]}[4] == -1) {
					if ($arg =~ /^([^\*]*)\*([^\*]*)$/) {
						$commandlinechange{$type}($1, $2);
						$implemented = 1;
					}
					else {
						printerror ("EF", "", $text, "outfile argument value invalid.\n".
						"  Possible argument values:\n".
						"    character string * character string\n".
						"    Ex. Gen*.c\n");
					}
				}
				if ($implemented == 0) {
					my $errormessage = "${$commandlinearguments[$i]}[0] argument value invalid.\n".
					"  Possible argument values:\n";
					my $number = ${$commandlinearguments[$i]}[4];
					if ($number == 0) {
						$number = 1;
					}
					for (my $j = 1; $j <= $number; $j++) {
						$errormessage = $errormessage . "    " . ${$commandlinearguments[$i]}[4+$j] . "\n";
					}
					printerror (${$commandlinearguments[$i]}[3], $text, $errormessage);
				}
			}
		}
		if ($implemented == 0) {
			my $errormessage = "Command line argument invalid.\n".
			"  Possible command line options:\n";
			for(my $j = 0; $j < scalar @commandlinearguments; $j++  ) {
				$errormessage = $errormessage . "    " . ${$commandlinearguments[$j]}[0] . "\n";
			}
			printerror ("EA", "", $text, $errormessage);
		}
		$text = $rest;
	}
	if ($text =~ /[\S]/) {
		printerror ("EB", "", $text, "Command line argument structure invalid.");
	}
}
# PARSING PHASE: Takes in a line, parses and processes all varlist args 
sub setvarlistargs {
	my $text = $_[0];
	$varlistvarname[scalar @varlistvarname] =  $varlistname[scalar @varlistname-1];
	$varlisttype[scalar @varlisttype] = "float";
	$varlistinitvalue[scalar @varlistinitvalue] = "";
	$varlistinitallflag[scalar @varlistinitallflag] = "0";
	$varlistendtouch[scalar @varlistendtouch] = "1";
	
	for (my $i = 0; $i < scalar @varlistarguments; $i++) {
		${$varlistarguments[$i]}[1] = 0;
	}
	
	while ($text =~ /^[\s]*(([\w]+)(\(([^\)]*)\))?)(.*)$/) {
		
		my $argmissingflag = 0;
		my $full = $1;
		my $type = $2;
		my $arg;
		
		if (defined $4 && $4 ne "") {
			$arg = $4;
		}
		else {
			$argmissingflag = 1;
		}
			
		my $rest = $5;
		
		my $implemented = 0;
		for (my $i = 0; $i < scalar @varlistarguments; $i++) {
			if ($type eq ${$varlistarguments[$i]}[0]) {
			#Check Duplicates
				if (${$varlistarguments[$i]}[1] == 1) {
					printerror (${$varlistarguments[$i]}[2], "", $text, "${$varlistarguments[$i]}[0] argument more than once.");
				}
				elsif ($i == 0 && ${$varlistarguments[1]}[1] == 1) {
					printerror (${$varlistarguments[$i]}[2], "", $text, "${$varlistarguments[$i]}[0] argument more than once.");
				}
				elsif ($i == 1 && ${$varlistarguments[0]}[1] == 1) {
					printerror (${$varlistarguments[$i]}[2], "", $text, "${$varlistarguments[$i]}[0] argument more than once.");
				}
				else {
					${$varlistarguments[$i]}[1] = 1;
				}
				if (${$varlistarguments[$i]}[4] > 0) {
					if ($argmissingflag == 1) {
						$varlistchange{$type}(${$varlistarguments[$i]}[5]);
						$implemented = 1;
					}
					else {
						for (my $j = 1; $j <= ${$varlistarguments[$i]}[4]; $j++) {
							if ($arg eq ${$varlistarguments[$i]}[4+$j]) {
								$varlistchange{$type}($arg);
								$implemented = 1;
							}		
						}
					}
				}
				elsif (${$varlistarguments[$i]}[4] == 0) {
					if ($argmissingflag == 1) {
						my $errormessage = "${$varlistarguments[$i]}[0] needs an argument value.\n".
						"  Possible argument values:\n";
						my $number = ${$varlistarguments[$i]}[4];
						if ($number == 0) {
							$number = 1;
						}
						for (my $j = 1; $j <= $number; $j++) {
							$errormessage = $errormessage . "    " . ${$varlistarguments[$i]}[4+$j] . "\n";
						}
						printerror ("CV", "", $text, $errormessage);
						
					}
					#Only accepts charstrings and _
					if ($arg =~ /[\w]+/) {
						$varlistchange{$type}($arg);
						$implemented = 1;
					} 						
				}
				if ($implemented == 0) {
					my $errormessage = "${$varlistarguments[$i]}[0] argument value invalid.\n".
					"  Possible argument values:\n";
					my $number = ${$varlistarguments[$i]}[4];
					if ($number == 0) {
						$number = 1;
					}
					for (my $j = 1; $j <= $number; $j++) {
						$errormessage = $errormessage . "    " . ${$varlistarguments[$i]}[4+$j] . "\n";
					}
					printerror (${$varlistarguments[$i]}[3], "", $text, $errormessage);
				}
			}
		}
		if ($implemented == 0) {
			my $errormessage = "Varlist argument invalid.\n".
			"  Possible Varlist options:\n";
			for(my $j = 0; $j < scalar @varlistarguments; $j++  ) {
				$errormessage = $errormessage . "    " . ${$varlistarguments[$j]}[0] . "\n";
			}
			printerror ("K", "", $text, $errormessage);
		}
		$text = $rest;
	}
	#Now picked up by Error K
	if ($text =~ /[\S]/) {
		printerror ("P", "", $text, "Varlist line argument structure invalid.");
	}
}
# PARSING PHASE: Takes in a line, parses and processes all value args
sub setvalueargs {
	my $text = $_[0];
	
	$parametersreportflag[scalar @parametersreportflag] = 0;
	$parametersnoreplaceflag[scalar @parametersnoreplaceflag] = 0;

	for (my $i = 0; $i < scalar @valuearguments; $i++) {
		${$valuearguments[$i]}[1] = 0;
	}
	
	while ($text =~ /^[\s]*(([\w]+)(\(([^\)]*)\))?)(.*)$/) {
		my $argmissingflag = 0;
		my $full = $1;
		my $type = $2;
		my $arg;
		
		if (defined $4 && $4 ne "") {
			$arg = $4;
		}
		else {
			$argmissingflag = 1;
		}
				
		 
		my $rest = $5;
		
		my $implemented = 0;
		for (my $i = 0; $i < scalar @valuearguments; $i++) {
			if ($type eq ${$valuearguments[$i]}[0]) {
				#Check Duplicates
				if (${$valuearguments[$i]}[1] == 1) {
					printerror (${$valuearguments[$i]}[2], "", $text, "${$valuearguments[$i]}[0] argument more than once.");
				}
				${$valuearguments[$i]}[1] = 1;
				if (${$valuearguments[$i]}[4] > 0) {
					if ($argmissingflag == 1) {
						$valuechange{$type}(${$valuearguments[$i]}[5]);
						$implemented = 1;
					}
					else {
						for (my $j = 1; $j <= ${$valuearguments[$i]}[4]; $j++) {
							if ($arg eq ${$valuearguments[$i]}[4+$j]) {
								$valuechange{$type}($arg);
								$implemented = 1;
							}		
						}
					}
				}
				elsif (${$valuearguments[$i]}[4] == 0) {
					if ($argmissingflag == 1) {
						my $errormessage = "${$valuearguments[$i]}[0] needs an argument value.\n".
						"  Possible argument values:\n";
						my $number = ${$valuearguments[$i]}[4];
						if ($number == 0) {
							$number = 1;
						}
						for (my $j = 1; $j <= $number; $j++) {
							$errormessage = $errormessage . "    " . ${$valuearguments[$i]}[4+$j] . "\n";
						}
						printerror ("CU", "", $text, $errormessage);
						
					}
					if ($arg) {
						$valuechange{$type}($arg);
						$implemented = 1;
					} 						
				}
				if ($implemented == 0) {
					my $errormessage = "${$valuearguments[$i]}[0] argument value invalid.\n".
					"  Possible argument values:\n";
					my $number = ${$valuearguments[$i]}[4];
					if ($number == 0) {
						$number = 1;
					}
					for (my $j = 1; $j <= $number; $j++) {
						$errormessage = $errormessage . "    " . ${$valuearguments[$i]}[4+$j] . "\n";
					}
					printerror (${$valuearguments[$i]}[3], "", $text, $errormessage);
				}
			}
		}
		if ($implemented == 0) {
			my $errormessage = "Value line argument invalid.\n".
			"  Possible value line options:\n";
			for(my $j = 0; $j < scalar @valuearguments; $j++  ) {
				$errormessage = $errormessage . "    " . ${$valuearguments[$j]}[0] . "\n";
			}
			printerror ("Z", "", $text, $errormessage);
		}
		$text = $rest;
	}
	#Now picked up by Error Z
	if ($text =~ /[\S]/) {
		printerror ("AA", "", $text, "Value line argument structure invalid.");
	}
}
# PARSING PHASE: Takes in a line, parses and processes all variable args
sub setvarargs {
	my $text = $_[0];
	
	$variablesreportflag[scalar @variablesreportflag] = 0;
	
	for (my $i = 0; $i < scalar @vararguments; $i++) {
		${$vararguments[$i]}[1] = 0;
	}
	
	while ($text =~ /^[\s]*(([\w]+)(\(([^\)]*)\))?)(.*)$/) {
		my $argmissingflag = 0;

		my $full = $1;
		my $type = $2;
		my $arg;
		if (defined $4 && $4 ne "") {
			$arg = $4;
		}
		else {
			$argmissingflag = 1;
		}
		my $rest = $5;
		
		my $implemented = 0;
		for (my $i = 0; $i < scalar @vararguments; $i++) {
			if ($type eq ${$vararguments[$i]}[0]) {
			#Check Duplicates
				if (${$vararguments[$i]}[1] == 1) {
					printerror (${$vararguments[$i]}[2], "", $text, "${$vararguments[$i]}[0] argument more than once.");
				}
				${$vararguments[$i]}[1] = 1;
				if (${$vararguments[$i]}[4] > 0) {
					if ($argmissingflag == 1) {
						$varchange{$type}(${$vararguments[$i]}[5]);
						$implemented = 1;
					}
					else {
						for (my $j = 1; $j <= ${$vararguments[$i]}[4]; $j++) {
							if ($arg eq ${$vararguments[$i]}[4+$j]) {
								$varchange{$type}($arg);
								$implemented = 1;
							}		
						}
					}
				}
				elsif (${$vararguments[$i]}[4] == 0) {
					if ($argmissingflag == 1) {
						my $errormessage = "${$vararguments[$i]}[0] needs an argument value.\n".
						"  Possible argument values:\n";
						my $number = ${$vararguments[$i]}[4];
						if ($number == 0) {
							$number = 1;
						}
						for (my $j = 1; $j <= $number; $j++) {
							$errormessage = $errormessage . "    " . ${$vararguments[$i]}[4+$j] . "\n";
						}
						printerror ("CW", "", $text, $errormessage);
						
					}
					if ($arg) {
						$varchange{$type}($arg);
						$implemented = 1;
					} 						
				}
				if ($implemented == 0) {
					my $errormessage = "${$vararguments[$i]}[0] argument value invalid.\n".
					"  Possible argument values:\n";
					my $number = ${$vararguments[$i]}[4];
					if ($number == 0) {
						$number = 1;
					}
					for (my $j = 1; $j <= $number; $j++) {
						$errormessage = $errormessage . "    " . ${$vararguments[$i]}[4+$j] . "\n";
					}
					printerror (${$vararguments[$i]}[3], "", $text, $errormessage);
				}
			}
		}
		if ($implemented == 0) {
			my $errormessage = "Variable line argument invalid.\n".
			"  Possible variable line options:\n";
			for(my $j = 0; $j < scalar @vararguments; $j++  ) {
				$errormessage = $errormessage . "    " . ${$vararguments[$j]}[0] . "\n";
			}
			printerror ("BA", "", $text, $errormessage);
		}
		$text = $rest;
	}
	#Now picked up by Error BA
	if ($text =~ /[\S]/) {
		printerror ("BB", "", $text, "Variable line argument structure invalid.");
	}
}
# PARSING PHASE: Takes in a line, parses and processes all feature args
sub setfeatureargs {
	my $text = $_[0];
	
	$featuressinglelineflag[scalar @featuressinglelineflag] = 0;
	
	for (my $i = 0; $i < scalar @featurearguments; $i++) {
		${$featurearguments[$i]}[1] = 0;
	}
	
	while ($text =~ /^[\s]*(([\w]+)(\(([^\)]*)\))?)(.*)$/) {
		my $argmissingflag = 0;
		my $full = $1;
		my $type = $2;
		my $arg;
		
		if (defined $4 && $4 ne "") {
			$arg = $4;
		}
		else {
			$argmissingflag = 1;
		}
		my $rest = $5;
		
		my $implemented = 0;
		for (my $i = 0; $i < scalar @featurearguments; $i++) {
			if ($type eq ${$featurearguments[$i]}[0]) {
			#Check Duplicates
				if (${$featurearguments[$i]}[1] == 1) {
					printerror (${$featurearguments[$i]}[2], "", $text, "${$featurearguments[$i]}[0] argument more than once.");
				}
				${$featurearguments[$i]}[1] = 1;
				if (${$featurearguments[$i]}[4] > 0) {
					if ($argmissingflag == 1) {
						$featurechange{$type}(${$featurearguments[$i]}[5]);
						$implemented = 1;
					}
					else {
						for (my $j = 1; $j <= ${$featurearguments[$i]}[4]; $j++) {
							if ($arg eq ${$featurearguments[$i]}[4+$j]) {
								$featurechange{$type}($arg);
								$implemented = 1;
							}		
						}
					}
				}
				elsif (${$featurearguments[$i]}[4] == 0) {
					if ($argmissingflag == 1) {
						my $errormessage = "${$featurearguments[$i]}[0] needs an argument value.\n".
						"  Possible argument values:\n";
						my $number = ${$featurearguments[$i]}[4];
						if ($number == 0) {
							$number = 1;
						}
						for (my $j = 1; $j <= $number; $j++) {
							$errormessage = $errormessage . "    " . ${$featurearguments[$i]}[4+$j] . "\n";
						}
						printerror ("BO", "", $text, $errormessage);
						
					}
					if ($arg) {
						$featurechange{$type}($arg);
						$implemented = 1;
					} 						
				}
				if ($implemented == 0) {
					my $errormessage = "${$featurearguments[$i]}[0] argument value invalid.\n".
					"  Possible argument values:\n";
					my $number = ${$featurearguments[$i]}[4];
					if ($number == 0) {
						$number = 1;
					}
					for (my $j = 1; $j <= $number; $j++) {
						$errormessage = $errormessage . "    " . ${$featurearguments[$i]}[4+$j] . "\n";
					}
					printerror (${$featurearguments[$i]}[3], "", $text, $errormessage);
				}
			}
		}
		if ($implemented == 0) {
			my $errormessage = "Feature line argument invalid.\n".
			"  Possible feature line options:\n";
			for(my $j = 0; $j < scalar @featurearguments; $j++  ) {
				$errormessage = $errormessage . "    " . ${$featurearguments[$j]}[0] . "\n";
			}
			printerror ("L", "", $text, $errormessage);
		}
		$text = $rest;
	}
	if ($text =~ /[\S]/) {
		#Shouldnt happen, captured by error N. Incase.
		printerror ("ZZG", "", $text, "Feature line argument structure invalid.");
	}
}

##?##?## PHASE2: TOOLBOX FUNCTIONS ##?##?##

# GENERATING PHASE: Returns 1 if number, 2 if string (with spaces), 0 otherwise
sub numbervsstring {
	my $text = $_[0];
	if ($text =~ /$interegex$/) {
		return 1;
	}
	elsif ($text =~ /^[\w\s]*$/) {
		return 2;
	}
	elsif ($text =~ /^[\'|\"](.*)[\'|\"]$/) {
		return 2;
	}
	else {
		return 0;
	}
}
# GENERATING PHASE: Check if the string is even a boolean statement
#Returns 1 if it is a possible boolean statement, 0 if it is not
#Not a perfect test
sub teststringisboolean {
	my $text = $_[0];
	
	if ($text =~ /^[\s]*$/) {
		return 0;
	}
	#Check if there are words separated by a space
	elsif ($text =~ /[\w] [\w]/) {
		return 0;
	}
	elsif ($text =~ /^([$ineqregex]*)$/) {
		return 1;
	}
	return 0;
}
# GENERATING PHASE: Check if the string is even a math statement
#Returns 1 if it is a possible math statement, 0 if it is not
#Not a perfect test
sub teststringismath {
	my $text = $_[0];
	if ($text =~ /^[\s]*$/) {
		return 0;
	}
	elsif ($text =~ /^[$mathregex\d\s\.]*$/) {
		return 1;
	}
	return 0;
}
# GENERATING PHASE: Eval a boolean statement. Returns 1 if true or 0 if false
sub evaluateboolean {
	my $inequality = $_[0];
	my $infeature = $_[1];
	
	#Test adding quotes to words
	#if ($inequality =~ /([A-Za-z]+)/) {
	#	$inequality =~ s/(^|[^\w"])([\w]+)([^\w"]|$)/$1"$2"$3/g;
	#	$inequality =~ s/"eq"/eq/g;
	#	$inequality =~ s/"ne"/ne/g;
	#	$inequality =~ s/"le"/le/g;
	#	$inequality =~ s/"lt"/lt/g;
	#	$inequality =~ s/"ge"/ge/g;
	#	$inequality =~ s/"gt"/gt/g;
	#}
	
	#replace distributions
	#printP (3, "The boolean we are checking is $inequality.\n");
	#If it is a boolean statement
	if (teststringisboolean($inequality) == 1) {
		#Evaluate it, if true, return 1
		if (eval($inequality)) {
			return 1;
		}
	}
	
	#Otherwise return 0
	return 0;
}
# GENERATION PHASE: Throw error if ranges in a dist arent properly defined

sub checkrangeerrors {
	my $dist = $_[0];
	my $start = $_[1];
	my $end = $_[2];
	for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		if ($start =~ /\$\{$parameters[$pariter]\}/) {
			if (!defined ${$parameterscounters[$currentdepth]}[$pariter]) {
				printerror ("BK", "", "Value $start in $dist", "Start value not defined yet.");
			}
			$start = ${$parameterscounters[$currentdepth]}[$pariter];
		}
		if ($end =~ /\$\{$parameters[$pariter]\}/) {
			if (!defined ${$parameterscounters[$currentdepth]}[$pariter]) {
				printerror ("BL", "", "Value $end in $dist", "End value not defined yet.");
			}
			$end = ${$parameterscounters[$currentdepth]}[$pariter];
		}
	}
	
}

sub throwrangeerror {
	my $dist = $_[0];
	my $range = $_[1];
	if ($range =~ /([-]?[$referegex]+)[\s]*:[\s]*([-]?[$referegex]+)/) {
		my $start = $1;
		my $end = $2;
		if ($start =~ /[^$mathregex\s\d]/) {
			printerror ("AU", "", "Value $start from $range in $dist", "Start value not a valid value to sample from.");
		}
		elsif ($end =~ /[^$mathregex\s\d]/) {
			printerror ("AV", "", "Value $end from $range in $dist", "End value not a valid value to sample from.");
		}
		elsif ($end < $start) {
			printerror ("BG", "", "Value $start:$end from $range in $dist", "End is less than start of range.");
		}
	}

	printerror ("ZZH", "", "$dist with $range", "Something is off with the compiler. Tell Alton.");
}
# GENERATION PHASE: if the feature needs to be in a single line
sub fixsingleline {
	my $text = $_[0];
	my $infeature = $_[1];
	
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
		if ($features[$feaiter] eq $infeature && $featuressinglelineflag[$feaiter] == 1) {
			$insingleline[$currentdepth] = 1;
		}
	}
	
	if ($insingleline[$currentdepth] > 0) {
		#remove all enters
		#$text =~ s/^[^\S\n]//;
		$text =~ s/\n[^\S\n]?//g;
	}
	
	return $text;
}

##?##?## PHASE2: SAMPLE LINES ##?##?##

# GENERATION PHASE: Checks if a line has a keyword to process
sub testLineForKeywords {
	my $text = $_[0];
	my $infeature = $_[1];
	if ($timingflag == 1 && $replacestarttime != 0) {
		if ($replaceendtime > $replacestarttime) {
			my $newreplaceendtime = time;
			$timereplace = $timereplace + ($newreplaceendtime - $replaceendtime);
			$replaceendtime = $newreplaceendtime;
		}
		else {
			$replaceendtime = time;
			$timereplace = $timereplace + ($replaceendtime - $replacestarttime);
		}
	}
	# Three slashes /// is a comment in Genesis
	if ($text =~ /^[\s]*\/\/\//){ 
		printP (3, "Comment. Do nothing.\n");
	}
	elsif ($text =~ /^[\s]*distribution/) {
		handleDistributionLine ($text, $infeature);
		lineCount(1);
	}
	elsif ($text =~ /^[\s]*value/) {
		handleValueLine($text, $infeature);
		lineCount(2);
	}
	elsif ($text =~ /^[\s]*varlist/) {
		handleVarlistLine($text, $infeature);
		lineCount(3);
	}
	elsif ($text =~ /^[\s]*variable/) {
		handleVariableLine($text, $infeature);
		lineCount(4);
	}
	elsif ($text =~ /^[\s]*stored/) {
		handleStoredLine($text, $infeature);
		lineCount(5);
	}	
	elsif ($text =~ /^[\s]*add/) {
		handleAddLine($text, $infeature);
		lineCount(6);
	}
	elsif ($text =~ /^[\s]*remove/) {
		handleRemoveLine($text, $infeature);
		lineCount(7);
		
	}
	elsif ($text =~ /^[\s]*genmath/) {
		handleGenmathLine($text, $infeature);
		lineCount(8);
	}

	elsif ($text =~ /^[\s]*genassert[\s]+([$refqregex]+)[\s]*$/) {
		printP (3, "ASSERT!");
		lineCount(9);
		print "$text";
		my $inequality = $1;
		$inequality = replaceGenesisNamesTop($inequality, $infeature, 1);

		if (evaluateboolean($inequality, $infeature)==0) {
			printG (2, "\nAssert Failed! $inequality");
			$badflag = 1;
		}
	}
	elsif ($ignorevertspaceflag == 1 && $text =~ /^[\s]*$/) {
		printP (3, "Do not include this line\n");
	}
	
	else {
		if ($timingflag == 1) {
			if ($replacestarttime == 0 || $replaceendtime > $replacestarttime) {
				$replacestarttime = time;
			}
			else {
				my $newreplacestarttime = time;
				$timereplace = $timereplace + ($newreplacestarttime - $replacestarttime);
				$replacestarttime = $newreplacestarttime;
			}
		}
		return 0;
	}
	if ($timingflag == 1) {
		if ($replacestarttime == 0 || $replaceendtime > $replacestarttime) {
			$replacestarttime = time;
		}
		else {
			my $newreplacestarttime = time;
			$timereplace = $timereplace + ($newreplacestarttime - $replacestarttime);
			$replacestarttime = $newreplacestarttime;
		}
	}
	return 1;
}
# GENERATION PHASE: Find a varlist line and perform the sampling
sub handleVarlistLine {
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	#find a searchid. If it is not eval, it equals another varlist and we need that ID. Otherwise, create/use the next ID.
	my $searchvalue;
	if ($varlistevalflag[$info] == 0){
		for (my $vliter2 = 0; $vliter2 < scalar @varlistname; $vliter2++) {
			if ($varlistname[$vliter2] eq $varlistequalvar[$info]) {
				$searchvalue = $vliter2;
				$varlistvarname[$info] = $varlistvarname[$vliter2];
				$varlistarg[$info] = $varlistarg[$vliter2];
			}
		}
		if (!defined $searchvalue) {
			printerror ("DG", "", "$varlistequalvar[$info]", "Varlist source does not exist.");
		}
	}
	else {
		$searchvalue = $info;
	}
	
	my $numberToAdd = replaceGenesisNamesTop($varlistarg[$searchvalue], $infeature, 0);
	
	#create varlist
	if ($numberToAdd =~ /^[\d]*$/) {

		#Add blank varlists to all varlists in the array
		for (my $i = scalar @varlistavailability; $i < $info; $i++) {
			my @varslist;
			$varlistavailability[$info] = \@varslist;
		}
		#add a varlist, initiate it all to 1
		my @varslist;
		for (my $i = 0; $i < $numberToAdd; $i++) {
			$varslist[scalar @varslist] = 1;
		}
		$varlistavailability[$info] = \@varslist;
		$varlistvalidity[$info] = $currentdepth;
	}
	else {
		printerror ("BF", "", "$varlistarg[$searchvalue]", "Value in the brackets not a number.");
	}
}
# GENERATION PHASE: Find a distribution line and call handleDistribution
sub handleDistributionLine {
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	handleDistribution($globaldistributions[$info],1, $infeature, 0);
}
# GENERATION PHASE: Find a distribution and add to valid dists
sub handleDistribution {
	my $distline = $_[0];
	my $underscorecheck = $_[1];
	my $infeature = $_[2];
	my $phase = $_[3];
	my $flag = 0;
	
	if ($distline =~ /^[\s]*[\w]*[\s]*=[\s]*\{[$generegex,:;\s]*\}[\s]*$/) {
		my @valuerange;
		my @value;
		my @prob;
		my @real;
		my $samplevar;
		my $range;
		my $distribute;
		($samplevar, $range) = split("=", $distline, 2);
		$samplevar =~ s/^\s+|\s+$//g;
		$range =~ s/^\s*{\s*|\s*}\s*$//g;
		
		#Variable Terminal Reporting
		my $output = adddepthspacing("Dist: $samplevar with range: $range\n");
		printG (3, "$output");
		
		if ($samplevar =~ /^_/) {
			if ($underscorecheck == 1) {
				printerror ("BI", "", $samplevar, "Underscores allowed but cannot be first char.");
			}
		}
		else {
			my $disthasavalflag = 0;
			
			#check if a distribution is a duplicate
			for (my $pariter = 0; $pariter < scalar @distributions; $pariter++) {
				if ($samplevar eq $distributions[$pariter]) {
					printerror ("BP", "", $samplevar, "Distribution used already.");
				}
			}
			
			#check if a distribution is unused
			for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
				if ($parametersevalflag[$pariter] == 1) {
					if ($samplevar eq $parametersdistvar[$pariter]) {
						$disthasavalflag = 1;
					}
				}
			}
			
			#check if a distribution is unused
			for (my $pariter = 0; $pariter < scalar @genmathdistvar; $pariter++) {
				if ($samplevar eq $genmathdistvar[$pariter]) {
					$disthasavalflag = 1;
				}
			}
			
			if ($disthasavalflag == 0) {
				printwarning ("WG", "", $samplevar, "Distribution declared but not used.");
			}
		}
		
		#separate values from the distributions
		($range, $distribute) = split(";;", $range, 2);

		my $divide = 1;
		my $real = 0;
		if (defined $distribute) {
			if ($distribute =~ /^real\((.*)\)$/) {
				$real = $1;
				if ($real =~ /([\d])/ && $real >= 0) {
					$divide = 0;
				}
				else {
					printerror ("DZ", "", $distribute, "Real argument invalid.");				
				}
				$distribute = "real";
			}
			elsif ($distribute =~ /^real$/) {
				$divide = 0;
				$real = 2;
			}
		}
		if ($phase == 1) {
			printP (2, "  Dist: '" .$samplevar . "'\n");
		}

		#separate values
		while ($range =~ /^([^,;\{]*|[^,;\{]*\{[^\$\{\}]*\})[,;](.*)$/) {
			my $current = $1;
			$range = $2;
			
			@valuerange[scalar @valuerange] = $current;
		}
		
		@valuerange[scalar @valuerange] = $range;
		
		my $probexistscheck = -1;
		
		my $probabilitysum = 0;

		for(my $i = 0; $i < scalar @valuerange; $i++) {
			$valuerange[$i] =~ s/^\s+|\s+$//g;
			my $distvalue;
			my $probabilityclause;
			my @probability;
			
			my $probabilityseen = 0;
			my $incrementseen = 0;
					
			if ($valuerange[$i] =~ /^((\$\{|[-\"\}$equaregex,:;\.\s])*)(\{[-$generegex,:;\.\%\s]*\})?$/) {
				$distvalue = $1;
				$probabilityclause = $3;
				
			}
				
			elsif ($valuerange[$i] =~ /^([\'|\"]($refqregex\s])*[\'|\"])(\{[-$generegex,:;\.\%\s]*\})?$/) {
				$distvalue = $1;
				$probabilityclause = $3;
			}
			
			else {
				printerror ("M2", "", $valuerange[$i], "Weird distribution value. Right chars, but format may be off.");
			}
		
			#Split if there is a clause
			if (defined $probabilityclause) {
				@probability = split(",", $probabilityclause);
			}
			#If not put a dummy
			else {
				$probability[0] = "";
			}
			
			if (scalar @probability > 2) {
				printerror ("BU", "", $valuerange[$i], "Too many probability arguments.");
			}
			
			my $increment = "+1";
			my $currentprobability = 100/scalar @valuerange;
			
			for(my $j = 0; $j < scalar @probability; $j++) {
				$probability[$j] =~ s/^\s*{\s*|\s*}\s*$//g;
				if (defined $probability[$j] && $probability[$j] =~ /[^$mathregex\d\.\s\%]/) {
					printerror ("BJ", "", $probability[$j], "Probability is non-numeric.");
				}
				#A probability
				if ($probability[$j] =~ /^([\d][^\%]*)[\%]?$/) {				
					my $cleanprob = $1;
					if ($probabilityseen == 1) {
						printerror ("BV", "", $valuerange[$i], "Too many probabilities.");
					}
					$probabilityseen = 1;
					
					if ($probexistscheck == -1 ) {
						$probexistscheck = 1;		
					}
					if (teststringismath($cleanprob)) {
						$currentprobability = eval($cleanprob);
					}
					else {
						printerror ("ZZI", "", "Prob of $cleanprob" , "Something is off with the compiler. Tell Alton.");
					}
					
				}
				#An increment
				elsif ($probability[$j] =~ /^[\.\s$mathregex]/) {
					if ($incrementseen == 1) {
						printerror ("BW", "", $valuerange[$i], "Too many increments.");
					}
					$incrementseen = 1;
					$increment = $probability[$j]; 
				}
			}
			
			$probabilitysum = $probabilitysum + $currentprobability;
			
			if ($probabilityseen == 0 && $probexistscheck == -1) {
				$probexistscheck = 2;
			}
			
			if ($probexistscheck == 2 && $probabilityseen == 1) {
				printerror ("DA", "", $distline, "Inconsistency. Either give probabilities to every entry in this distribution, or use no probabilities at all.");
			}
			if ($probexistscheck == 1 && $probabilityseen == 0) {
				printerror ("DB", "", $distline, "Inconsistency. Either give probabilities to every entry in this distribution, or use no probabilities at all.");
			}
					
			#range with colon
			if ($distvalue =~ /^(.+)[\s]*:[\s]*(.+)$/) {
			
				my $start = $1;
				my $end = $2;
				
				checkrangeerrors($samplevar, $start, $end);
				$start = replaceGenesisNamesTop($start, $infeature, 0);
					
				$end = replaceGenesisNamesTop($end, $infeature, 0);
					
				if (teststringismath($start)) {
					$start = eval($start);
				}
				
				if (teststringismath($end)) {
					$end = eval($end);
				}
					
				#should be numbers
				if (numbervsstring($start)==1 && numbervsstring($end)==1) {
					if ($end < $start) {
						printerror ("J", "", $distline, "Dist range end less than start value.");
					}
					if (defined $distribute && lc($distribute) eq "real") {
						$value[scalar @value] = "$start:$end";
						$prob[scalar @prob] = "real";
						$real[scalar @real] = $real;
					}
					else {
						#add an entry for every value in the range
						for(my $entry = $start; $entry < $end+1;) {
							$value[scalar @value] = $entry;
							if (defined $distribute && lc($distribute) eq "uniform") {
								$prob[scalar @prob] = 100/(scalar @valuerange*($end-$start+1));
								$real[scalar @real] = 0;
							}
							elsif (teststringismath($currentprobability)) {
								$prob[scalar @prob] = eval($currentprobability)/($end-$start+1);
								$real[scalar @real] = 0;
							}
							else {
								#Shouldnt happen, captured by error BJ if userdeclared. Incase.
								printerror ("ZZJ", "", "Prob of $currentprobability" , "Something is off with the compiler. Tell Alton.");
							}
						
							my $math = $entry.$increment;
							
							if (teststringismath($math)) {
								$entry = eval($math);
							}
							else {
								#Shouldnt happen, captured by error BJ if userdeclared. Incase.
								printerror ("ZZK", "", "Prob of $increment" , "Something is off with the compiler. Tell Alton.");
							}
						}
					}
				}
				# Likely an error if the chars are still in
				else {
					throwrangeerror($samplevar, $distvalue);
					#Should not reach this point
					printerror ("ZZL", "", "$distline" , "Something is off with the compiler. Tell Alton.");
				}
			}
			
			#A word or char string, added quotes
			elsif ($distvalue =~ /^([-]?[\"\w]+)$/ || $distvalue =~ /^([\'|\"][$refqregex]+[\'|\"])$/) {
			
				#Replace the names
				$distvalue = replaceGenesisNamesTop($distvalue, $infeature, 0);
			
				$value[scalar @value] = $1;
				if (defined $currentprobability && $currentprobability =~ /^[\d]/) {
					$prob[scalar @prob] = $currentprobability;
					$real[scalar @real] = 0;
				}
				elsif (defined $distribute && lc($distribute) eq "uniform") {
					$prob[scalar @prob] = 100/scalar @valuerange;
					$real[scalar @real] = 0;
				}
				else {
					$prob[scalar @prob] = 100/scalar @valuerange;
					$real[scalar @real] = 0;
				}
			}
			
			#Error if it makes it here
			else {
				if ($distvalue =~ /^([-]?[\d]+)[\s]*-[\s]*([-]?[\d]+)$/ || $distvalue =~ /^([-]?[\w]+)[\s]*-[\s]*([-]?[\w]+)$/) {
					printerror ("M", "", $valuerange[$i], "Quite possibly using the old distribution method. Fix: Change dashes (-) to colons (:).");
				}
				printerror ("M", "", $valuerange[$i], "Weird distribution value. Right chars, but format may be off.");
			}
		}
		
		if (!(($probabilitysum > 0.99 && $probabilitysum < 1.01) || ($probabilitysum > 99 && $probabilitysum < 101))) {
			printerror ("DC", "", "Prob sum of $probabilitysum", "Probabilities not between 99 and 101.");
		}
		
		#Normalize as necessary so probabilities sum up to 1
		if ($divide == 1) {
			my $probsum = 0;
			for(my $i = 0; $i < scalar @prob; $i++) {
				if (teststringismath($prob[$i])) {
					$probsum = $probsum + eval($prob[$i]);
				}
				else {
					#Shouldnt happen, captured by error BJ if userdeclared. Incase.
					printerror ("ZZM", "", "Prob of $prob[$i]" , "Something is off with the compiler. Tell Alton.");
				}
			}
			
			for(my $i = 0; $i < scalar @prob; $i++) {
				if (teststringismath($prob[$i])) {
					$prob[$i] = eval($prob[$i])/$probsum;
				}
				else {
					#Shouldnt happen, captured by error BJ if userdeclared. Incase.
					printerror ("ZZN", "", "Prob of $prob[$i]" , "Something is off with the compiler. Tell Alton.");
				}
			}
		}
		$distributionsvalues[scalar @distributionsvalues] = \@value;
		$distributionsprob[scalar @distributionsprob] = \@prob;
		$distributionsreal[scalar @distributionsreal] = \@real;
		$distributions[scalar @distributions] = $samplevar;
		if ($phase == 1) {
			printP (2, "		For $samplevar:\n");
			for(my $i = 0; $i < scalar @value; $i++) {
				printP (2, "		Range: '" . $value[$i] ."' with Distribution: '". $prob[$i]. "'\n");
			}
		}

	}
	elsif ($distline =~ /^[\s]*$/) {
		#New F warning
		#printwarning ("WF", "", $distline, "Empty Distribution.");
		
	} 
	else {
		printerror ("O", "", $distline, "Weird distribution value. Some char not allowed.");
	}
}
# GENERATION PHASE: Find a value line and perform the sampling
sub handleValueLine {
#Parse
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	for(my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		if ($parametersnumber[$pariter] eq $info) {
			my $samplevar = $parameters[$pariter];
			my $valuenumber = $info;
			$samplevar =~ s/^\s+|\s+$//g;

			my $bracketnum;
			if ($parametersarrayflag[$pariter] == 1) {
				$bracketnum = replaceGenesisNamesTop($parametersarraybrackets[$pariter], $infeature, 0);
				$bracketnum =~ s/^\s+|\s+$//g;
				# The way this is implemented, the square brackets needs a set number, cannot be a Genesis value,  but at this point all genesis values should have been replaced anyway
				if (numbervsstring($bracketnum) != 1) {
					printerror ("R", "", "Value $parameters[$pariter] with num $bracketnum", "Number for value array is invalid.");
				}
				elsif ($parametersarraybrackets[$pariter] ne "") {
					my @valuearray;
					for(my $arriter = 0; $arriter < $bracketnum; $arriter++){
						$valuearray[$arriter] = "";
					}
					${$parameterscounters[$currentdepth]}[$pariter] = \@valuearray;
				}
				#Shouldnt happen, captured by error Q. Incase.
				else {
					printerror ("DP", "", "$parametersarraybrackets[$pariter]", "Nothing in the brackets.");
				}
			}
			# else, not an array
			else {
				$bracketnum = -1;
			}
			#Enumerating
			if ($parametersfullflag[$pariter] == 1) {
				my $defined = 0;
				my $sampledflag = 0;
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {
						$defined = 1;
						${$parameterscounters[$currentdepth]}[$pariter] = ${$distributionsvalues[$disiter]}[0]; 
						${$parameterssampled[$currentdepth]}[$pariter] = 1;
						printG (3, "$parameters[$pariter] replace to ${$parameterscounters[$currentdepth]}[$pariter] \n");
						if ($parametersreportflag[$pariter]==1 && $parametersfullflag[$pariter]==1) {
							$valuereportedflag = 1;
							reportvalue($pariter);
						}
						$sampledflag = 1;
						last;
					}
				}
				if ($sampledflag == 0) {
					printerror ("DO", "", "Value '$samplevar' with distribution '$parametersdistvar[$pariter]'", "Dist for this value does not exist for enumerate.");
				}
			}
			#Sampling (as opposed to =)
			elsif ($parametersevalflag[$pariter]==1) {
				#If this is the first value (alone, or with noreplace)
				if ($currentreplace != $parametersnoreplaceflag[$pariter] || $parametersnoreplaceflag[$pariter] == 0) {
					@sampledalready = ();
					$currentreplace = $parametersnoreplaceflag[$pariter];
				}
				my $sampledflag = 0;
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					#Found the corresponding distribution
					if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {

						#Value Terminal Reporting
						my $output = adddepthspacing("Value Sampling $parameters[$pariter] = ");
						printG (3, "$output");
						
						#If it is not a real distribution (no real modifier)
						if (${$distributionsprob[$disiter]}[0] ne "real") {
							my $sampledcorrectly = 0;
							my $i = 0;
							for(my $arriter = 0; $arriter < $bracketnum || $bracketnum == -1; $arriter++){
								if ($currentreplace != $parametersnoreplaceflag[$pariter] || $parametersnoreplaceflag[$pariter] == 0) {
									@sampledalready = ();
									$currentreplace = $parametersnoreplaceflag[$pariter];
								}
								$sampledcorrectly = 0;
								while ($sampledcorrectly == 0) {
									#Check if there are not enough values to sample
									if (scalar @sampledalready == scalar @{$distributionsprob[$disiter]}) {
										printerror ("Y", "", "Value $samplevar with distribution $parametersdistvar[$pariter]", "Not enough distribution to sample all without replacement (" . scalar @sampledalready . " vs " . scalar @{$distributionsprob[$disiter]} . ").");
									}
									#calculate a random probability
									my $randomprob = rand();
									my $runningprob = 0;
									#determine where it indexes to
									for ($i = 0; $runningprob < $randomprob; $i++) {
										$runningprob = $runningprob + ${$distributionsprob[$disiter]}[$i];
									}
									
									#See if it's an array
									if ($bracketnum != -1) {
										${${$parameterscounters[$currentdepth]}[$pariter]}[$arriter] = ${$distributionsvalues[$disiter]}[$i - 1];
									}
									else {
										#set the values and say we sampled it
										${$parameterscounters[$currentdepth]}[$pariter] = ${$distributionsvalues[$disiter]}[$i - 1];
									}
									${$parameterssampled[$currentdepth]}[$pariter] = 1;
									$sampledcorrectly = 1;
									#see if it is already sampled (i.e., noreplace)
									#for now, make sure its not an array
									
									if($parametersarrayflag[$pariter] == 0) {
										for (my $j = 0; $j < scalar @sampledalready; $j++) {
										
											if (${$parameterscounters[$currentdepth]}[$pariter] eq $sampledalready[$j]){
												#so it stays in while loop to sample again
												$sampledcorrectly = 0;
											}
										}
									}
									#if it was still sampled correct, add to sampled already list in case of noreplace
									if ($sampledcorrectly == 1) {
										$sampledalready[scalar @sampledalready] = ${$parameterscounters[$currentdepth]}[$pariter];
									}
								}
								#Report the value
								if ($parametersreportflag[$pariter]==1 && $parametersfullflag[$pariter]==0) {
									$valuereportedflag = 1;
									reportvalue($pariter);
								}
								
								#increase global counters
								if ($printGlobalcountersflag == 1 || $chisquaredtestflag == 1) {
									${$parametersglobalcounter[$pariter]}[$i-1]++;
								}
								if ($printlocalcountersflag == 1) {
									if ($currentdepth == 0) {
										#${$parametersstartcounter[$pariter]}[$i-1]++;
									}
									else {
										#${$parameterslocalcounter[$pariter]}[$i-1]++;
									}
								}
								if ($bracketnum == -1) {
									$bracketnum = 0;
								}
							}
						}
						#Real sampling
						else { 
							if (${$distributionsvalues[$disiter]}[0] =~ /([-\d]*):([\d]*)/) {
								my $start = $1;
								my $end = $2;	
								#Just get a random value
								my $result = (rand($end-$start))+$start;
								${$parameterscounters[$currentdepth]}[$pariter] = sprintf "%.".${$distributionsreal[$disiter]}[0]."f", $result;
								
								${$parameterssampled[$currentdepth]}[$pariter] = 1;
							}	
							#Report the value
							if ($parametersreportflag[$pariter]==1) {
								$valuereportedflag = 1;
								reportvalue($pariter);
							}
						}
						#If we make it here, we've sampled it
						printG (3, "${$parameterscounters[$currentdepth]}[$pariter]\n");
						$sampledflag = 1;
					}
				}
				#Should be taken by Error H
				if ($sampledflag == 0) {
					printerror ("H", "", "Value '$samplevar' with distribution '$parametersdistvar[$pariter]'", "Dist for this value does not exist.");
				}
			}
			#No sampling, just initializing
			elsif ($parametersdistvar[$pariter] eq "" && $parametersequalpar[$pariter] eq "") {
				#Initialize but not sample
				${$parameterssampled[$currentdepth]}[$pariter] = 0;
			}
			#=	
			else {
				my $replacetext = $parametersequalpar[$pariter];	
				$replacetext = replaceGenesisNamesTop($replacetext, $infeature, 0);
				
				#Value Terminal Reporting
				my $output = adddepthspacing("Value Sampling $parameters[$pariter] = ");
				printG (3, "$output");
						
				#If math, evaluate
				if (teststringismath($replacetext)) {
					$replacetext = (eval($replacetext));
				}
				#If it is a string of chars, leave it alone
				elsif (numbervsstring($replacetext) == 2) {
				}
				else {
					# Should be captured by distribution checks
					printerror ("DE", "", "$replacetext" , "String has characters. Put it around quotes or fix the reference.");
				}
				
				#store the value
				${$parameterscounters[$currentdepth]}[$pariter] = $replacetext;
				${$parameterssampled[$currentdepth]}[$pariter] = 1;
				printG (3, " ${$parameterscounters[$currentdepth]}[$pariter]\n");
			}
		}
	}
}

# GENERATION PHASE: Find a stored line and perform the processing
sub handleStoredLine {
#Parse
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	for(my $pariter = 0; $pariter < scalar @stored; $pariter++) {
		if ($storednumber[$pariter] eq $info) {
			my $valuenumber = $info;
			
			for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
				if ($features[$feaiter] eq $storedvar[$pariter]) {
					my @tempfunction;
					for (my $funiter = 0; $funiter < scalar @{$featureslist[$feaiter]}; $funiter++) {
						my $text = ${$featureslist[$feaiter]}[$funiter];						
						#Process the feature
						if (!testLineForKeywords($text, $features[$feaiter])) {	
							lineCount(12);
							$tempfunction[scalar @tempfunction] = searchForReferences($text, $features[$feaiter]);
						}				
					}
					${$storedsampled[$currentdepth]}[$feaiter] = 1;
					$storedprocessed[$pariter]  = \@tempfunction;
					for (my $funiter = 0; $funiter < scalar @tempfunction; $funiter++) {
						printP (3, "   Feature line $funiter: $tempfunction[$funiter]");
					}
				}
			}
		
		}
	}
}
# GENERATION PHASE: Find a genmath line and perform the action
sub handleGenmathLine {
#Parse
	my $text = $_[0];
	my $infeature = $_[1];
	
	my $keyword;
	my $wholestring;
	
	my $samplevar;
	my $replacetext;
	
	my $bracketnum;
	
	$text = replaceGenesisNamesTop($text, $infeature, 0);

	
	($keyword, $wholestring) = split(" ", $text, 2);

	$wholestring =~ s/^\s+|\s+$//g;
	#Added a negative sign
	
	if ($wholestring =~  /^([\w\[\]]*)[\s]*=[\s]*([\'|\"]?[\$\(\w\-][$generegex\s\"\'\.]*)$/) {
		$samplevar = $1;
		$replacetext = $2;

		if ($samplevar =~ /^([\w]*)\[([\w]*)\]/ ) {
			$samplevar = $1;
			$bracketnum = $2;
		}
		else {
			$bracketnum = -1;
		}
		
		#Replace values in the RHS
		$replacetext = replaceGenesisNamesTop($replacetext, $infeature, 0);
		
		#else, only do it if its mathable. no chars allowed!
		if (teststringismath($replacetext)) {
			$replacetext = (eval($replacetext));
		}
		else {
			# assuming just characters are okay...
			if ($replacetext =~ /^[\w]*$/) {
			}
			#quotes are okay too
			elsif ($replacetext =~ /^[\'|\"](.*)[\'|\"]$/) {
				$replacetext = $1;
			}
			#so stuff like "blab+boo" are invalid
			else {
				printerror ("V", "", "RHS of expression '$replacetext'", "RHS or expression not fully evaluated.");
			}
		}
		
		#Replace the left hand side parameter
		my $sampled = 0;
		for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
			if ($parametersfeature[$pariter] eq $infeature || $parametersfeature[$pariter] eq "") {
				if ($samplevar eq $parameters[$pariter]) {
					my $tempdepth = $currentdepth;
					# sampled at 1, 0 are every step above
					#ex "" "" 1 0 0 0
					while ($tempdepth >= 0 && ${$parameterssampled[$tempdepth]}[$pariter] ne "") {
						if ($bracketnum != -1) {
							${${$parameterscounters[$tempdepth]}[$pariter]}[$bracketnum] = $replacetext;
						}
						else {
							${$parameterscounters[$tempdepth]}[$pariter] = $replacetext;
						}
						${$parameterssampled[$tempdepth]}[$pariter] = 0;

						$tempdepth--;
					}
					if ($bracketnum != -1) {
						${${$parameterscounters[$tempdepth+1]}[$pariter]}[$bracketnum] = $replacetext;
					}
					else {
						${$parameterscounters[$tempdepth+1]}[$pariter] = $replacetext;

					}
					${$parameterssampled[$tempdepth+1]}[$pariter] = 1;
					$sampled = 1;
				}
			}
		}
		for (my $loopiter = 0; $loopiter < scalar @genloopvar; $loopiter++) {
			if ($genloopfeature[$loopiter] eq $infeature) {
				if ($genloopvalid[$loopiter] >= 1) {
					if ($samplevar eq $genloopvar[$loopiter]) {
						${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1] = $replacetext;
						$sampled = 1;
					}
				}
			}			
		}
		if ($sampled == 0) {
			printerror ("W", "", "Value $samplevar", "LHS does not exist to genmath.");
		}
		
	}
	
	elsif($wholestring =~ /^([$referegex,\s]*)[\s]+sample[\s]+([$equaregex]+)(.*)$/ || $wholestring =~ /^([$referegex,\s]*)[\s]+sample[\s]+{[-$generegex,:;\s]*}(.*)$/ ) {
	
		my $range;
		my $args; 
		# Value sampling
		if ($wholestring =~ /^([\w,$referegex\s]*)[\s]+sample[\s]+([$equaregex]+)(.*)$/) {
			$samplevar = $1;
			$range = $2;
			$args = $3;
		}
		#Value sampling with in-line distributions
		elsif ($wholestring =~ /^([\w,$referegex\s]*)[\s]+sample[\s]+({[-$generegex,:;\s]*})(.*)$/) {
			$samplevar = $1;
			
			my $tempdistname = "_a" . scalar @localdistributions;
			$range = $tempdistname;
			my $tempdist = $tempdistname . " = " . $2;
			$localdistributions[scalar @localdistributions] = $tempdist;
			handleDistribution($tempdist, 0, "", 0);
			$args = $3;
		}
		
		if ($samplevar =~ /^([\w]*)\[([\w]*)\]/ ) {
			$samplevar = $1;
			$bracketnum = $2;
		}
		else {
			$bracketnum = -1;
		}
		
		#Replace the left hand side parameter
		my $sampled = 0;
		for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
			if ($parametersfeature[$pariter] eq $infeature || $parametersfeature[$pariter] eq "") {
				if ($samplevar eq $parameters[$pariter]) {
				
					#If this is the first value (alone, or with noreplace)
					if ($currentreplace != $parametersnoreplaceflag[$pariter] || $parametersnoreplaceflag[$pariter] == 0) {
						@sampledalready = ();
						$currentreplace = $parametersnoreplaceflag[$pariter];
					}
				
					#Figure out value, put in replace text. Copied for now.
					my $sampledflag = 0;
					for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
						#Found the corresponding distribution
						if ($distributions[$disiter] eq $range) {

							#Value Terminal Reporting
							my $output = adddepthspacing("Value Sampling $parameters[$pariter] = ");
							printG (3, "$output");
							
							#If it is not real
							if (${$distributionsprob[$disiter]}[0] ne "real") {
								my $sampledcorrectly = 0;
								my $i = 0;
								while ($sampledcorrectly == 0) {
									#Check if there are not enough values to sample
									if (scalar @sampledalready == scalar @{$distributionsprob[$disiter]}) {
										printerror ("Y", "", "Value $samplevar with distribution $range", "Not enough distribution to sample all without replacement (" . scalar @sampledalready . "sampled already vs " . scalar @{$distributionsprob[$disiter]} . "in dist).");
									}
									#calculate a random probability
									my $randomprob = rand();
									my $runningprob = 0;
									#determine where it indexes to
									for ($i = 0; $runningprob < $randomprob; $i++) {
										$runningprob = $runningprob + ${$distributionsprob[$disiter]}[$i];
									}
									
									$replacetext = ${$distributionsvalues[$disiter]}[$i - 1];
									${$parameterssampled[$currentdepth]}[$pariter] = 1;
									$sampledcorrectly = 1;
									
									#see if it is already sampled (i.e., noreplace)
									for (my $j = 0; $j < scalar @sampledalready; $j++) {
										if ($replacetext eq $sampledalready[$j]){
											#so it stays in while loop to sample again
											$sampledcorrectly = 0;
										}
									}
									#if it was still sampled correct, add to sampled already list in case of noreplace
									if ($sampledcorrectly == 1) {
										$sampledalready[scalar @sampledalready] = $replacetext;
									}
								}
								
								#Report the value
								if ($parametersreportflag[$pariter]==1 && $parametersfullflag[$pariter]==0) {
									$valuereportedflag = 1;
									reportvalue($pariter);
								}
								
								#increase global counters
								if ($printGlobalcountersflag == 1 || $chisquaredtestflag == 1) {
									${$parametersglobalcounter[$pariter]}[$i-1]++;
								}
								if ($printlocalcountersflag == 1) {
									if ($currentdepth == 0) {
										#${$parametersstartcounter[$pariter]}[$i-1]++;
									}
									else {
										#${$parameterslocalcounter[$pariter]}[$i-1]++;
									}
								}
							
							}
							#Real sampling
							else { 
								if (${$distributionsvalues[$disiter]}[0] =~ /([-\d]*):([\d]*)/) {
									my $start = $1;
									my $end = $2;	
									#Just get a random value
									$replacetext = (rand($end-$start))+$start;
									${$parameterssampled[$currentdepth]}[$pariter] = 1;
								}	
								#Report the value
								if ($parametersreportflag[$pariter]==1) {
									$valuereportedflag = 1;
									reportvalue($pariter);
								}
							}
							#If we make it here, we've sampled it
							printG (3, "$replacetext\n");
							$sampledflag = 1;
						}
					}
					#Should be taken by Error H
					if ($sampledflag == 0) {
						printerror ("DN", "", "Value '$samplevar' with distribution '$range'", "Distribution in genmath statement does not exist.");
					}				
							
				
					#Replacement goes here
					my $tempdepth = $currentdepth;
					while ($tempdepth >= 0 && ${$parameterssampled[$tempdepth]}[$pariter] ne "") {
					
						#See if it's an array
						if ($bracketnum != -1) {
						
							${${$parameterscounters[$currentdepth]}[$pariter]}[$bracketnum] = $replacetext;
						}
						else {
							${$parameterscounters[$tempdepth]}[$pariter] = $replacetext;
						}
						$tempdepth--;
					}
					$sampled = 1;
				}
			}
		}
		if ($sampled == 0) {
			printerror ("DM", "", "Value '$samplevar' with distribution '$range'", "The LHS value does not exist.");
		}
	}
	else {
		printerror ("U", "", "Value '$wholestring'", "Genmath string not valid.");
	}
}
# GENERATION PHASE: Find a variable line and perform the sampling
sub handleVariableLine {
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	for(my $variter = 0; $variter < scalar @variables; $variter++) {
		if ($variablesnumber[$variter] eq $info) {		
			my $varnametouse;
			#If taken from varlist
			if ($variablesevalflag[$variter]==1) {
				my $varlisttouse = replaceGenesisNamesTop($variablesvarlistvar[$variter], $infeature, 0);
				my $sampled = 0;
				for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
				
					if ($varlistname[$vliter] eq $varlisttouse) {
					
						if ($varlistvalidity[$vliter] == -1) {
							printerror ("CM", "", $varlistname[$vliter], "Varlist was not initiated yet.");
						}
						$varnametouse = $varlisttouse;
						${$variablescounters[$currentdepth]}[$variter] = int(rand(scalar @{$varlistavailability[$vliter]}))+1;
						#test empty, if empty, print warning
						my $isempty = 1;
						for (my $i = 0; $i < scalar @{$varlistavailability[$vliter]}; $i++) {
						
							if (${$varlistavailability[$vliter]}[$i] == 1) {
								$isempty = 0;
							}
						}
						#If it is not empty, then sample until one that is available is sampled
						if ($isempty == 0) {
							while (${$varlistavailability[$vliter]}[${$variablescounters[$currentdepth]}[$variter]-1] == 0) {
								${$variablescounters[$currentdepth]}[$variter] = int(rand(scalar @{$varlistavailability[$vliter]}))+1;
							}
						}
						else {
							#Error replaced with a warning for empty varlists
							printwarning ("WDD", "", "'$variables[$variter]' from $varlistname[$vliter]", "Sampling from an Empty Varlist.");
							$badflag = 2;
						}
						$sampled = 1;
						
						#Variable Terminal Reporting
						my $output = adddepthspacing("(Varlist of " . scalar @{$varlistavailability[$vliter]} .") Var Sampling $variables[$variter] = $varlistvarname[$vliter]${$variablescounters[$currentdepth]}[$variter] \n");
						printG (3, "$output");

					}
				}
				if ($sampled == 0) {
					printerror ("I", "", "Variable $variables[$variter] with distribution '$variablesvarlistvar[$variter]'", "Varlist for this variable does not exist.");
				}
			}
			#If taken from another value
			else {
			
				${$variablescounters[$currentdepth]}[$variter] = $variablesequalpar[$variter];
						
				for (my $variter2 = 0; $variter2 < scalar @variables; $variter2++) {
					if (${$variablescounters[$currentdepth]}[$variter] =~ /\$\{$variables[$variter2]\}/) {
						#Use their varname and their value
						$varnametouse = $variablesvarlistvar[$variter];
						${$variablescounters[$currentdepth]}[$variter] =~ s/\$\{$variables[$variter2]\}/${$variablescounters[$currentdepth]}[$variter2]/;
					}
				}
				
				if (teststringismath(${$variablescounters[$currentdepth]}[$variter])) {
					${$variablescounters[$currentdepth]}[$variter] = eval(${$variablescounters[$currentdepth]}[$variter]);
				}
				#Should be captured by Error BT.
				else {
					printerror ("ZZO", "", "$variablesequalpar[$variter]" , "Not a valid varstring math result.");
				}
				
				#Make sure the variable after math is in the varlist
				for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
					if ($varlistname[$vliter] eq $variablesvarlistvar[$variter]) {
						my $maxvalue = scalar @{$varlistavailability[$vliter]};
						my $value = ${$variablescounters[$currentdepth]}[$variter];
						${$variablescounters[$currentdepth]}[$variter] = ((eval($value)-1)%$maxvalue)+1;
					}
				}
			}
			#Report it
			if ($variablesreportflag[$variter]==1) {
				$valuereportedflag = 1;
				reportvariable($variter, $varnametouse);
			}
			
		}
	}

}
# GENERATION PHASE: Find a add line and add variables to varlists
sub handleAddLine {
	printG (3, ' AddVariable!'. "\n");
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	for(my $additer = 0; $additer < scalar @addvariables; $additer++) {
		if ( $addvariablesnumber[$additer] eq $info) {
			my $toaddvar;
			my $toadddist;
			
			my $varlisttouse = replaceGenesisNamesTop($addvariablesvarlistvar[$additer], $infeature, 0);
			
			#Add All
			if ($addvariables[$additer] eq "all") {
				for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
					if ($varlisttouse eq $varlistname[$vliter]) {
						
						if ($varlistvalidity[$vliter] == -1) {
							printerror ("CS", "", $varlistname[$vliter], "Varlist was not initiated yet for add all.");
						}
					
						for (my $i = 0; $i < scalar @{$varlistavailability[$vliter]}; $i++) {
							${$varlistavailability[$vliter]}[$i] = 1;
							printG (3, " adding all to $varlisttouse\n");
						}
					}
				}
			}
			#Otherwise add 1
			else {
				#Add a number
				if ($addvariables[$additer] =~ /^[0-9]+$/) {
					$toaddvar = $addvariables[$additer]-1;
					$toadddist = $addvariables[$additer];
					printG (3, " adding $addvariables[$additer] to $varlisttouse\n");
				}
				#Add a value
				else {
					for (my $variter = 0; $variter < scalar @variables; $variter++) {
						if ($addvariables[$additer] eq $variables[$variter] && ($variablesfeature[$variter] eq $infeature || $variablesfeature[$variter] eq "")) {
						
							$toaddvar = ${$variablescounters[$currentdepth]}[$variter]-1;
							$toadddist = ${$variablescounters[$currentdepth]}[$variter];
							printG (3, " adding $variables[$variter] 's ${$variablescounters[$currentdepth]}[$variter] to $varlisttouse\n");
		
						}
					}
					for (my $variter = 0; $variter < scalar @parameters; $variter++) {
						if ($addvariables[$additer] eq $parameters[$variter] && ($parametersfeature[$variter] eq $infeature || $parametersfeature[$variter] eq "")) {
							$toadddist = ${$parameterscounters[$currentdepth]}[$variter];
							$toaddvar = ${$parameterscounters[$currentdepth]}[$variter];
							printG (3, " adding $parameters[$variter] 's ${$parameterscounters[$currentdepth]}[$variter] to $varlisttouse\n");
				
						}
					}
					for (my $loopiter = 0; $loopiter < scalar @genloopvar; $loopiter++) {
						if ($genloopfeature[$loopiter] eq $infeature) {
							if ($addvariables[$additer] eq $genloopvar[$loopiter] && $genloopvalid[$loopiter] >= 1) {
								$toaddvar = ${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1]-1;
								$toaddvar = ${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1];
								print (2, " adding $genloopvar[$loopiter] 's $toaddvar to $varlisttouse\n");
							}
						}
					}
				}
			
				#The actual add to the availability list
				for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
					if ($varlisttouse eq $varlistname[$vliter]) {
						if ($varlistvalidity[$vliter] == -1) {
							printerror ("CQ", "", $varlistname[$vliter], "Varlist was not initiated yet for add.");
						}
					
						${$varlistavailability[$vliter]}[$toaddvar] = 1;
						printG (3, "  add successful!");
					}
				}
				
				#The actual add to the distribution
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					if ($distributions[$disiter] eq $varlisttouse) {
						if (${$distributionsprob[$disiter]}[0] ne "real") {
		
							my $size = scalar @{$distributionsprob[$disiter]};
							my $total = 1 + 1/$size;
							
							#Add new value
							${$distributionsvalues[$disiter]}[scalar @{$distributionsvalues[$disiter]}] = $toadddist;
							
							#add distributions
							${$distributionsprob[$disiter]}[scalar @{$distributionsprob[$disiter]}] = 1/$size;
							${$distributionsreal[$disiter]}[scalar @{$distributionsreal[$disiter]}] = 0;
							
							for (my $i = 0; $i < scalar @{$distributionsprob[$disiter]}; $i++) {
								${$distributionsprob[$disiter]}[$i] = ${$distributionsprob[$disiter]}[$i]/$total;
							}
							
							printG (3, " adding $addvariables[$additer] to $distributions[$disiter]\n");
							
						}
						else { 
							printerror ("BQ", "", $varlisttouse, "Add cannot work with real values.");
						}
					}
				}
			}
		}
	}
}
# GENERATION PHASE: Find a add line and remove variables from varlists
sub handleRemoveLine {
	#Remove variables from varlists
	printG (3, ' RemVariable!'. "\n");
	my $text = $_[0];
	my $infeature = $_[1];
	my $keyword;
	my $info;
	($keyword, $info) = split(" ", $text, 2);
	$info =~ s/^\s+|\s+$//g;
	for(my $remiter = 0; $remiter < scalar @remvariables; $remiter++) {
		if ($remvariablesnumber[$remiter] eq $info) {
			my $toremvar;
			my $toremdist;
			my $varlisttouse = replaceGenesisNamesTop($remvariablesvarlistvar[$remiter], $infeature, 0);

			#Remove All
			if ($remvariables[$remiter] eq "all") {
				for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
								
					if ($varlisttouse eq $varlistname[$vliter]) {
					
						if ($varlistvalidity[$vliter] == -1) {
							printerror ("CT", "", $varlistname[$vliter], "Varlist was not initiated yet for remove all.");
						}
					
						for (my $i = 0; $i < scalar @{$varlistavailability[$vliter]}; $i++) {
							${$varlistavailability[$vliter]}[$i] = 0;
							printG (3, " removing all to $varlisttouse\n");
							
						}
					}
				}
			}
			#Remove 1
			else {
				#Remove a number
				if ($remvariables[$remiter] =~ /^[0-9]+$/) {
					$toremvar = $remvariables[$remiter]-1;
					$toremdist = $remvariables[$remiter];
					printG (3, " removing $remvariables[$remiter] to $varlisttouse\n");
				}
				#Remove a value
				else {
					for (my $variter = 0; $variter < scalar @variables; $variter++) {
						if ($remvariables[$remiter] eq $variables[$variter] && ($variablesfeature[$variter] eq $infeature || $variablesfeature[$variter] eq "")) {
							$toremvar = ${$variablescounters[$currentdepth]}[$variter]-1;
							$toremdist = ${$variablescounters[$currentdepth]}[$variter];
							
							printG (3, " removing $variables[$variter] 's ${$variablescounters[$currentdepth]}[$variter] from $varlisttouse\n");
						}
					}
					for (my $variter = 0; $variter < scalar @parameters; $variter++) {
						if ($remvariables[$remiter] eq $parameters[$variter] && ($parametersfeature[$variter] eq $infeature || $parametersfeature[$variter] eq "")) {
							$toremdist = ${$parameterscounters[$currentdepth]}[$variter];
							$toremvar = ${$parameterscounters[$currentdepth]}[$variter];
							printG (3, " reming $variables[$variter] 's ${$variablescounters[$currentdepth]}[$variter] from $varlisttouse\n");
						}
					}
					for (my $loopiter = 0; $loopiter < scalar @genloopvar; $loopiter++) {
						if ($genloopfeature[$loopiter] eq $infeature) {
							if ($remvariables[$remiter] eq $genloopvar[$loopiter] && $genloopvalid[$loopiter] >= 1) {
								$toremvar = ${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1]-1;
								$toremvar = ${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1];
								printG (3, " reming $variables[$loopiter] 's ${$variablescounters[$currentdepth]}[$loopiter] from $varlisttouse\n");
							}
						}
					}
				}
			
				#The actual remove from the availability list
				for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
				
					if ($varlisttouse eq $varlistname[$vliter]) {
					
						if ($varlistvalidity[$vliter] == -1) {
							printerror ("CR", "", $varlistname[$vliter], "Varlist was not initiated yet for remove.");
						}
					
						${$varlistavailability[$vliter]}[$toremvar] = 0;
						printG (3, "  rem successful!\n");
					}
				}
				
				#The actual remove from the distribution
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					if ($distributions[$disiter] eq $varlisttouse) {
						if (${$distributionsprob[$disiter]}[0] ne "real") {
		
							for (my $i = 0; $i < scalar @{$distributionsvalues[$disiter]}; $i++) {
							
								if (${$distributionsvalues[$disiter]}[$i] == $remvariables[$remiter]) {
									my $total = 1 - ${$distributionsprob[$disiter]}[$i];
									
									${$distributionsprob[$disiter]}[$i] = 0;
									${$distributionsreal[$disiter]}[$i] = 0;
									
									for (my $j = 0; $j < scalar @{$distributionsvalues[$disiter]}; $j++) {
									
										${$distributionsprob[$disiter]}[$j] = ${$distributionsprob[$disiter]}[$j]/$total;
										
									}
								}								
							}
					
							printG (3, " removing $remvariables[$remiter] to $distributions[$disiter]\n");
							
						}
						else { 
								printerror ("BR", "", $varlisttouse, "Remove cannot work with real values.");
						}
					}
				}
			}
		}
	}
}

##?##?## PHASE2: REPLACE LINES ##?##?##

# GENERATION PHASE: Pushup values to next depth level
sub pushupValueDepth {
	my @parameterscounterlocal;
	my @parameterssampledlocal;
	
	#TODO: passing up and down should deep copy for arrays

	for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		$parameterscounterlocal[$pariter] = ${$parameterscounters[$currentdepth-1]}[$pariter];
		if (!defined ${$parameterssampled[$currentdepth-1]}[$pariter] || ${$parameterssampled[$currentdepth-1]}[$pariter] eq "") {
			$parameterssampledlocal[$pariter] = "";
		}
		else {
			$parameterssampledlocal[$pariter] = 0;
		}
		
	}
	$parameterscounters[$currentdepth] = \@parameterscounterlocal;
	$parameterssampled[$currentdepth] = \@parameterssampledlocal;
}
# GENERATION PHASE: Pushup variables to next depth level
sub pushupVariableDepth {
	my @variablescounterlocal;
	for (my $variter = 0; $variter < scalar @variables; $variter++) {
		$variablescounterlocal[$variter] = ${$variablescounters[$currentdepth-1]}[$variter];
	}
	$variablescounters[$currentdepth] = \@variablescounterlocal;
}
# GENERATION PHASE: Increase depth and all the things that go with it
sub increaseDepth {
	$currentdepth++;
	$distvalidlocality[$currentdepth] = scalar @distributions;
	$insingleline[$currentdepth] = $insingleline[$currentdepth-1];
	$lastlevelflag = 1;
	$currentindent[$currentdepth] = $currentindent[$currentdepth-1];
	pushupValueDepth();
	pushupVariableDepth();
}
# GENERATION PHASE: Decrease depth, clean up lists
sub decreaseDepth {
	#remove unneeded distributions
	while ($distvalidlocality[$currentdepth] != scalar @distributions) {
		splice(@distributions, scalar @distributions-1, 1);
		splice(@distributionsvalues, scalar @distributionsvalues-1, 1);
		splice(@distributionsprob, scalar @distributionsprob-1, 1);
		splice(@distributionsreal, scalar @distributionsreal-1, 1);
	}
	
	#Remove unneeded varlists
	for (my $vliter = 0; $vliter < scalar @varlistname; $vliter++) {
		if ($varlistvalidity[$vliter] eq $currentdepth) {
			my @varslist;
			$varlistavailability[$vliter] = \@varslist;
			$varlistvalidity[$vliter] = -1;
		}
	}
	
	$insingleline[$currentdepth+1] = 0;
	
	$currentdepth--;
}

##?##?## REPLACEMENT LINES ##?##?##

# GENERATION PHASE: Replace all genesis names that have to do with strings
sub replaceGenesisNames {
	my $replacetext = $_[0];	
	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $inequalityflag = $_[4];
	if ($referencereplaced == 0) {
		$replacetext = replaceFeatureParameters($replacetext, $reference, $referencename, $infeature, $inequalityflag);
	}
	if ($referencereplaced == 0) {
		$replacetext = replaceGenloopsVariables($replacetext, $reference, $referencename, $infeature, $inequalityflag);
	}
	if ($referencereplaced == 0) {
		$replacetext = replaceValueReferences($replacetext, $reference, $referencename, $infeature, $inequalityflag);
	}
	if ($referencereplaced == 0) {
		$replacetext = replaceVarlistReferences($replacetext, $reference, $referencename, $infeature, $inequalityflag);
	}
	if ($referencereplaced == 0) {
		$replacetext = replaceVariableReferences($replacetext, $reference, $referencename, $infeature, $inequalityflag);
	}

	return $replacetext;
}

sub replaceGenesisNamesTop {
	my $replacetext = $_[0];	
	my $infeature = $_[1];
	my $inequalityflag = $_[2];
	if ($timingflag == 1) {
		if ($replacestarttime == 0 || $replaceendtime > $replacestarttime) {
			$replacestarttime = time;
		}
		else {
			my $newreplacestarttime = time;
			$timereplace = $timereplace + ($newreplacestarttime - $replacestarttime);
			$replacestarttime = $newreplacestarttime;
		}
	}
	
	while ($badflag == 0 && $replacetext =~ /(^|[^\\])(\$\{([^\$\{\}]*)\})/) {
	
		my $reference = $2;
		my $referencename = $3;
		
		$referencereplaced = 0;

		$replacetext = replaceGenesisNames($replacetext, $reference, $referencename, $infeature, $inequalityflag);
		
		if ($referencecheck == 1 && $referencereplaced == 0) {
			printerror ("DH2", "", $referencename, "Reference found with a non-existent Genesis name.");
		}
		$referencereplaced = 0;
	}
	if ($timingflag == 1) {
		if ($replaceendtime > $replacestarttime) {
			my $newreplaceendtime = time;
			$timereplace = $timereplace + ($newreplaceendtime - $replaceendtime);
			$replaceendtime = $newreplaceendtime;
		}
		else {
			$replaceendtime = time;
			$timereplace = $timereplace + ($replaceendtime - $replacestarttime);
		}
	}
	return $replacetext;
}
# GENERATION PHASE: Replace all varlist references
sub replaceVarlistReferences {
	my $text = $_[0];	
	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $inequalityflag = $_[4];
		
	#replace distributions
	if ($referencename =~ /^([^\s\(\[]*)[^\S\n]*(\((.*)\))?[^\S\n]*(\[(.*)\])?$/) {
		my $referencename2 = $1;
		$referencename2 =~ s/^\s+|\s+$//g;

		my $bracketnum;
		my $parameterslist;
		
		if (defined $3) {
			$parameterslist = $3;
			$parameterslist =~ s/^\s+|\s+$//g;
		} 
		
		if (defined $5) {
			$bracketnum = $5;
			$bracketnum =~ s/^\s+|\s+$//g;
		}
		
		for (my $vliter = 0; $badflag == 0 && $vliter < scalar @varlistname; $vliter++) {
			if  ($referencename2 eq $varlistname[$vliter]) {
			
				lineCount(16);
			
				my $replace;
				if ((!defined $parameterslist || $parameterslist eq "size") && !defined $bracketnum) {
					my $counter = 0;
					for (my $i = 0; $i < scalar @{$varlistavailability[$vliter]}; $i++) {
						if (${$varlistavailability[$vliter]}[$i] == 1) {
							$counter++;
						}
					}
					
					$replace = $counter;
				}
				
				elsif (defined $parameterslist && $parameterslist eq "name") {
					$replace = $varlistvarname[$vliter];
				}
				#Check bracket bounds
				#TODO: check init all values
				elsif (defined $parameterslist && $parameterslist eq "value") {
					if (!defined $bracketnum) {
						printerror ("DY", "", "$reference", "Value arg needs an index.");
					}
					if (numbervsstring($bracketnum) == 2) {
						printerror ("DV", "", "$reference", "Varlist's Value arg not a number.");
					}
					elsif ($bracketnum > scalar @{$varlistavailability[$vliter]}) {
						printerror ("DW", "", "$reference", "Number for value arg of varlist is out of bounds: over.\nRemember indices for varlists start at 1.");
					}
					elsif ($bracketnum <= 0) {
						printerror ("DX", "", "$reference", "Number for value arg of varlist is out of bounds: under.\nRemember indices for varlists start at 1.");
					}
					
					else {
						if ($varlistinitallflag[$vliter]) {
							$replace = $varlistinitvalue[$vliter];
						}
						else {
							my @values = split(",", $varlistinitvalue[$vliter], 2);
							if (defined $values[$bracketnum]) {
								$replace = $values[$bracketnum];
							}
							else {
								$replace = 0;
							}
						}
					}
				}
				
				elsif (defined $parameterslist) {
					printerror ("DI", "", $parameterslist, "Not a proper argument for a varlist.");
				}
				
				else {
					$replace = $varlistvarname[$vliter] . $bracketnum;
				}
				
				#Strict made it not work before because eval(chars) is not defined with strict.

				#If it is in a genif, add quotes to the genloop variable
				if ($inequalityflag == 1) {
					$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/\"$1\"/;
				}
				else {
					$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/$1/;
				}
				
				my $before;
				my $end;
				
				$referencename = fixBracketsForRegEx($referencename);
				
				if ($text =~ /(^|[^\\])\$\{$referencename\}/) {
					if (defined $1) {
						$before = $1;
					}
					else {
						$before = "";
					}
					#Things are replaced once. removed /g.
					$text =~ s/(^|[^\\])\$\{$referencename\}/$before$replace/;
				}
				else {
					printerror ("ZZP", "", $text, "Something is off with the compiler. Tell Alton.");
				}
			
				$referencereplaced = 1;
				#debug_printcurrentparameterset;
				if (!defined $replace) {
					printerror ("ZZQ", "", $text, "Something is off with the compiler. Tell Alton.");
				}
			}
			$text =~ s/\\$varlistname[$vliter]/$varlistname[$vliter]/g;
		}
	}
	return $text;
}

sub checkTemplateValues {
	my $text = $_[0];
	for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
		if ($text =~ /^$parameters[$pariter]$/) {
			printerror ("BH", "", $text, "Feature repetition value not allowed in template program.");
		}
	}
}

sub fixBracketsForRegEx {
	my $text = $_[0];
	$text =~ s/\(/\\\(/g;
	$text =~ s/\)/\\\)/g;
	$text =~ s/\[/\\\[/g;
	$text =~ s/\]/\\\]/g;
	$text =~ s/\*/\\\*/g;
	$text =~ s/\//\\\//g;
	$text =~ s/\-/\\\-/g;
	$text =~ s/\=/\\\=/g;
	$text =~ s/\+/\\\+/g;
	return $text;		
}

# GENERATION PHASE: Replace all value references
sub replaceValueReferences {
	my $text = $_[0];
	my $reference = $_[1];
	my $referencename = $_[2];	
	my $infeature = $_[3];
	my $inequalityflag = $_[4];
	my $arrayflag = 0;
	my $bracketnum = -1;
		
	if ($referencename =~ /^([\w]*)\[([\d]*)\]/ ) {
		$referencename = $1;
		$bracketnum = $2;
		$arrayflag = 1;
		
		if (!defined $bracketnum || $bracketnum eq "") {
			printerror ("DQ", "", "$reference", "No number used for array value.");
		}
	}
	elsif ($referencename =~ /^([\w]*)\[(-[\d]*)\]/ ) {
		printerror ("DT", "", "$reference", "Number is out of bounds: under.\nRemember indices for value arrays start at 0.");
	}
	
	#replace distributions
	for (my $pariter = 0; $badflag == 0 && $pariter < scalar @parameters; $pariter++) {
		if ($referencename eq $parameters[$pariter]) {
			#Check if this value is in the template code (not allowed for now) 
			if ($infeature eq "" && (($referencecheck == 1 && $referencereplaced == 0) || $referencecheck == 0)){
				#if it is, this function will end processing
				checkTemplateValues($referencename);
			}
			#else check we're in the right feature and the value is defined
			elsif (($parametersfeature[$pariter] eq $infeature || $parametersfeature[$pariter] eq "") && (defined ${$parameterssampled[$currentdepth]}[$pariter])) {
				if (${$parameterssampled[$currentdepth]}[$pariter] ne "") {
					my $tempdepth = $currentdepth;
					# sampled at 1, 0 are every step above
					#ex "" "" 1 0 0 0

					while ($tempdepth >= 0 && ${$parameterssampled[$tempdepth]}[$pariter] eq "0") {
						$tempdepth--;
					}
					
					if ($tempdepth != -1 && ${$parameterssampled[$tempdepth]}[$pariter] eq "" && ${$parameterssampled[$tempdepth+1]}[$pariter] eq "0" && !defined ${$parameterscounters[$currentdepth]}[$pariter] ) {
						printerror ("DJ", "", $text, "Value used exists but has no sampled value yet.");
					}
					elsif ($tempdepth == -1 && ${$parameterssampled[0]}[$pariter] eq "0" && !defined ${$parameterscounters[$currentdepth]}[$pariter]){
						if ($equalWithoutGenmathFlag == 0) {
							printerror ("DK", "", $text, "Value used in global or program section and exists but has no sampled value yet.");
						}
						else {
							printerror ("DK1", "", $text, "Value used in global or program section and exists but has no sampled value yet. (Did you forget a genmath when assigning a value?)");
						}
					}
					
					lineCount(14);
					
					#Take what value replaces the reference
					my $replace;
					if ($parametersarrayflag[$pariter] == 1) {
					
						if ($arrayflag == 1) {
							if ($bracketnum >= scalar @{${$parameterscounters[$currentdepth]}[$pariter]}) {
								printerror ("DS", "", "Array $parameters[$pariter] with index $parametersarraybrackets[$pariter]", "Number is out of bounds: over. (value is $bracketnum while size is " . scalar @{${$parameterscounters[$currentdepth]}[$pariter]} .").\nRemember indices for value arrays start at 0.");
							}
							else {
								$replace = ${${$parameterscounters[$currentdepth]}[$pariter]}[$bracketnum];
							}
						}
						else {
							printerror ("DU", "", "$reference", "No index brackets used for array value.");
						}						
					}
					else {
						if ($arrayflag == 1) {
							printerror ("DR", "", "$parametersarraybrackets[$pariter]", "Number used for non-array value.");
						}
						else {
							$replace = ${$parameterscounters[$currentdepth]}[$pariter];
						}
					}
					#Strict made it not work before because eval(chars) is not defined with strict.
						
					if ($inequalityflag == 1) {
						$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/\"$1\"/;
					}
					else {
						$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/$1/;
					}
					
					my $before;
					my $end;
					
					$referencename = fixBracketsForRegEx($referencename);
					if ($text =~ /(^|[^\\])\$\{$referencename(\[$bracketnum\])?\}/) {
					
						if (defined $1) {
							$before = $1;
						}
						else {
							$before = "";
						}
												
						#Things are replaced once. removed /g.
						$text =~ s/(^|[^\\])\$\{$referencename(\[$bracketnum\])?\}/$before$replace/;
					}

					else {
						printerror ("ZZR", "", $text, "Something is off with the compiler. Tell Alton.");
					}
					
					$referencereplaced = 1;
					#debug_printcurrentparameterset;
					if (!defined $replace) {
						printerror ("ZZS", "", $text, "Something is off with the compiler. Tell Alton.");
					}
				}
			}
		}

		$text =~ s/\\$parameters[$pariter]/$parameters[$pariter]/g;
	}
	return $text;
}
# GENERATION PHASE: Replace all variable references
sub replaceVariableReferences {
	my $text = $_[0];
	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $inequalityflag = $_[4];
	
	for (my $variter = 0; $badflag == 0 && $variter < scalar @variables; $variter++) {
		if ($variablesfeature[$variter] eq $infeature) {
			if ($referencename eq $variables[$variter]) {
				my $varitersearch;
				my $varlisttouse;
				my $value;
				if ($variablesevalflag[$variter]==1) {
					$varitersearch = $variter;
					$varlisttouse = replaceGenesisNamesTop($variablesvarlistvar[$varitersearch], $infeature, 0);
					$value = "$reference";
				}
				#=
				else {
					for (my $variter2 = 0; $badflag == 0 && $variter2 < scalar @variables; $variter2++) {
						if ($variablesequalpar[$variter] =~ /$variables[$variter2]/) {			
							$varitersearch = $variter2;
														
							$value = $variablesequalpar[$variter];
							#printG (3, "Value for before $variables[$variter]: $variablesvarlistvar[$variter]\n");

							#$value =~ s/$variables[$variter2]/$variablesequalpar[$variter2]/;
							$variablesvarlistvar[$variter] = $variablesvarlistvar[$variter2];
							
							$varlisttouse = replaceGenesisNamesTop($variablesvarlistvar[$varitersearch], $infeature, 0);
							
							#printG (3, "Value for after $variables[$variter]: $variablesvarlistvar[$variter]\n");
						}
					}
				}
				
				#Find the varlist to know the name of the varlist, and replace
				for (my $vliter = 0; $badflag == 0 && $vliter < scalar @varlistname; $vliter++) {
					if ($varlistname[$vliter] eq $varlisttouse) {
						my $varnametouse;
						if ($varlistevalflag[$vliter] != 0){
							$varnametouse = $varlistvarname[$vliter];
						}
						else {
							$varnametouse = $varlistequalvar[$vliter];
						}
						$value =~s/\$\{$variables[$varitersearch]\}/${$variablescounters[$currentdepth]}[$varitersearch]/;

						my $maxvalue = scalar @{$varlistavailability[$vliter]};
						
						if (teststringismath($value)) {
							$value = ((eval($value)-1)%$maxvalue)+1;
							${$variablescounters[$currentdepth]}[$variter] = $value;
						}
						else {
							printerror ("ZZT", "", "$value" , "Something is off with the compiler. Tell Alton.");
						}
							
						lineCount(15);
						if ($inequalityflag == 1) {
							$text =~ s/(^|[^\\])\$\{$referencename\}/\"$1$varnametouse$value\"/g;
						}
						else {
							$text =~ s/(^|[^\\])\$\{$referencename\}/$1$varnametouse$value/g;
						}

						$referencereplaced = 1;
					}
				}
			}
		}
		$text =~ s/\\$variables[$variter]/$variables[$variter]/g;

	}
	return $text;
}
# GENERATION PHASE: Replace all stored feature references
sub replaceStoredReferences {
	my $text = $_[0];
	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $currentlastlevelflag = 1;
	#replace distributions
	for (my $pariter = 0; $pariter < scalar @stored; $pariter++) {
		if (($storedfeature[$pariter] eq $infeature && defined ${$storedsampled[$currentdepth]}[$pariter] && ${$storedsampled[$currentdepth]}[$pariter] ne "") || $storedfeature[$pariter] eq "") {
			if ($referencename eq $stored[$pariter]) {	
				#Work on spacing
				if ($currentlastlevelflag == 1 && $text =~ /^([^\S\n]*)/) {
				
					my $space = $1;
					#if ($infeature ne "" && $space =~ /^([\t])([^\S\n]*)/)
					#	$space = $2;
					#
					$currentindent[$currentdepth] = $currentindent[$currentdepth] . $space;
				}
								
				lineCount(17);				
				$currentlastlevelflag = 0;
	
	
				my $replacetext = "";
				for (my $funiter = 0; $funiter < scalar @{$storedprocessed[$pariter]}; $funiter++) {
					my $addtext = ${$storedprocessed[$pariter]}[$funiter];
					$addtext = searchForReferences($addtext, $infeature, 0);
					#$addtext =~ s/(^|\n)/$1$currentindent[$currentdepth]/g;
					#$addtext =~ s/$currentindent[$currentdepth]$//g;
										
					if ($addtext ne "" && (($lastlevelflag == 1 && $insingleline[$currentdepth] == 0) ||
					(defined $insingleline[$currentdepth+1] && $insingleline[$currentdepth+1] == 1 && $insingleline[$currentdepth] == 0))) {
						#$addtext =~ s/^/$currentindent[$currentdepth]/;
						#Case: reference[2] is put in 1 line, each needs an indent
						$addtext =~ s/\n/\n$currentindent[$currentdepth]/g;
						$addtext =~ s/\n[^\S\n]*$/\n/;

						#$text = $currentindent[$currentdepth] . $text;
					}
					
					$replacetext = $replacetext . $addtext;
					
				}
				
				my $before;
				my $end;
				
				$text =~ s/^([^\S\n]*)//;

										
				if ($text =~ /(^|[^\\])\$\{$referencename\}/) {
				
					if (defined $1) {
						$before = $1;
					}
					else {
						$before = "";
					}

					$replacetext =~ s/\n$//;
					
					#Things are replaced once. removed /g.
					$text =~ s/(^|[^\\])\$\{$referencename\}/$before$replacetext/;
				}

				else {
					printerror ("ZZU", "", $text, "Something is off with the compiler. Tell Alton.");
				}
				
				$referencereplaced = 1;
			}
		}
		
		if ($currentlastlevelflag == 0) {
			$lastlevelflag = 0;
		}
		
		$text =~ s/\\$stored[$pariter]/$stored[$pariter]/g;
	}
	return $text;
}
# GENERATION PHASE: Replace all genloop iterator references
sub replaceGenloopsVariables {
	my $text = $_[0];
	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $inequalityflag = $_[4];

	for (my $loopiter = 0; $loopiter < scalar @genloopvar; $loopiter++) {
		if ($genloopfeature[$loopiter] eq $infeature || $genloopfeature[$loopiter] eq "") {
			if ($genloopvalid[$loopiter] >= 1) {
				my $replace = ${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1];
				
				#If it is in a genif, add quotes to the genloop variable
				if ($inequalityflag == 1) {
					$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/\"$1\"/;
				}
				else {
					$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/$1/;
				}
				
				if  ($referencename eq $genloopvar[$loopiter]) {
					
					lineCount(22);
					
					if ($text =~ /(^|[^\\])\$\{$genloopvar[$loopiter]\}/) {
						$text =~ s/(^|[^\\])\$\{$genloopvar[$loopiter]\}/$1$replace/g;
					}
					else {
						$text =~ s/(^|[^\w\\])$genloopvar[$loopiter]($|\W)/$1$replace$2/g;
					}
					$referencereplaced = 1;
				}
			}
			$text =~ s/\\$genloopvar[$loopiter]/$genloopvar[$loopiter]/g;
		}
	}
	return $text;
}
# GENERATION PHASE: Replace all feature parameter references
sub replaceFeatureParameters {
	my $text = $_[0];
	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $inequalityflag = $_[4];

	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
		if ($infeature eq $features[$feaiter]) {
			if ($featuresparams[$feaiter] != 0) {
				for (my $pariter = 0; $pariter < scalar @{$featuresparams[$feaiter]}; $pariter++) {
					my $replace = ${${$featuresparameterlist[$feaiter]}[$featuresparamsvalid[$feaiter]-1]}[$pariter];
					
					#If it is in a genif, add quotes to the feature variable
					if ($inequalityflag == 1) {
						$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/\"$1\"/;
					}
					else {
						$replace =~ s/^[\'|\"]([$generegex,:;]*)[\'|\"]$/$1/;
					}	
					
					my $counter = 0;
					$counter++ while ($text =~ /(^|[^\\])\$\{${$featuresparams[$feaiter]}[$pariter]\}/g);

					my $counter2 = 0;
					if  ($referencename eq ${$featuresparams[$feaiter]}[$pariter]) {
						
						lineCount(19);
					
						$counter2++;
						$text =~ s/(^|[^\\])\$\{$referencename\}/$1$replace/;
						$referencereplaced = 1;
						if ($counter2 > $counter) {
							printerror ("DF", "", "\$\{${$featuresparams[$feaiter]}[$pariter]\}", "Probably an endless loop of replacement.");
						}					
					}
				}
			}
		}
	}
	return $text;
}

sub generateOnDemand {
	my $text = $_[0];
	my $bracketnum = $_[1];
	my $feaiter = $_[2];
	my $replacetext = "";
	
	for (my $i = 0; $badflag == 0 && $i < $bracketnum; $i++) {
		increaseDepth();

		my $textatnum = "";
		$featuresvalid[$feaiter] = 1;
		
		#Cycle the lines and search lines for references
		for (my $funiter = 0; $badflag == 0 && $funiter < scalar @{$featureslist[$feaiter]}; $funiter++) {
			my $text = ${$featureslist[$feaiter]}[$funiter];

			#re-sample
			if (!testLineForKeywords($text, $features[$feaiter])) {
				$text = searchForReferences($text, $features[$feaiter]);					
				$textatnum = $textatnum . $text;
			}
		}

		$featuresvalid[$feaiter] = 0;
		
		if ($textatnum ne "" && (($lastlevelflag == 1 && $insingleline[$currentdepth] == 0) ||
		(defined $insingleline[$currentdepth+1] && $insingleline[$currentdepth+1] == 1 && $insingleline[$currentdepth] == 0))) {
			#TODO: check: Which case needs this?
			#$textatnum =~ s/^/$currentindent[$currentdepth]/;
			#$text =~ s/\n/\n$currentindent[$currentdepth]/g;
			#$text = $currentindent[$currentdepth] . $text;
		}
		
		$replacetext = $replacetext . $textatnum;
		
		decreaseDepth();
	}
	return $replacetext;
}


# GENERATION PHASE: Replace all feature references
sub replaceFeatureReferences {

	if ($dotcounter % 10 == 0) {
		printG (2, ".");
		$dotcounter = 0;
	}
	$dotcounter++;

	my $text = $_[0];

	my $reference = $_[1];
	my $referencename = $_[2];
	my $infeature = $_[3];
	my $currentlastlevelflag = 1;
	
	if ($referencename =~ /^([^\s\(\[]*)[^\S\n]*(\((.*)\))?[^\S\n]*(\[(.*)\])?$/) {

		my $referencename2 = $1;
		$referencename2 =~ s/^\s+|\s+$//g;

		my $bracketnum;
		my $parameterslist;
		
		if (defined $3) {
			$parameterslist = $3;
		} 
		
		if (defined $5) {
			$bracketnum = $5;
			$bracketnum =~ s/^\s+|\s+$//g;
		}
		if (!defined $bracketnum) {
			$bracketnum = 1;
		}

		for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
			if ($referencename2 eq $features[$feaiter]) {
				#Check for no recursion
				if ($recursionflag == 0) {
					if ($infeature eq $features[$feaiter]) {
						printerror ("CO", "", "$infeature", "$infeature has recursion. Either turn on recursion flag or remove it completely.");
					}
				}
				
				if ($featuresvalid[$feaiter] == 1) {
					printerror ("CP", "", "$features[$feaiter]", "$features[$feaiter] has circular recursion. Either turn on recursion flag or remove it completely.");
				}
				
				printG (3, "$features[$feaiter] reference found.\n");
					
				#Work on spacing
				if ($currentlastlevelflag == 1 && $text =~ /^([^\S\n]*)/) {
				
					my $space = $1;
					#if ($infeature ne "" && $space =~ /^([\t])([^\S\n]*)/)
					#	$space = $2;
					#
					$currentindent[$currentdepth] = $currentindent[$currentdepth] . $space;
				}
				$currentlastlevelflag = 0;
				
				my @parameterlist;
				
				if (defined $parameterslist && scalar @{$featuresparams[$feaiter]} != 0) {
					@parameterlist = split(",", $parameterslist);
					for (my $i = 0; $i < scalar @parameterlist; $i++) {
						$parameterlist[$i] =~ s/^\s+|\s+$//g;
						$parameterlist[$i] = replaceGenesisNamesTop($parameterlist[$i], $infeature, 0);

					}
				}
				
				${$featuresparameterlist[$feaiter]}[$featuresparamsvalid[$feaiter]] = \@parameterlist;
				
				$featuresparamsvalid[$feaiter]++;

				if (scalar @parameterlist > scalar @{$featuresparams[$feaiter]}) {
					printerror ("S", "", $text, "Too many parameters in this feature.");
				}
				elsif (scalar @parameterlist < scalar @{$featuresparams[$feaiter]}) {
					printerror ("T", "", $text, "Too few parameters in this feature.");
				}
				
			
				#Added during May 27 reordering
				#Replace names in brackets
				$bracketnum = replaceGenesisNamesTop($bracketnum, $infeature, 0);

				lineCount(18);
				
				#Evaluate
				my $replacetext = "";
				if (teststringismath($bracketnum)) {
					$bracketnum = eval($bracketnum);
				}
				else {
					printerror ("G", "", $text, "Feature repetition value/number not valid.");
				}

				#Generate on Demand
				#my $replacetext = generateOnDemand($text, $bracketnum, $feaiter);
				
				#Do that many feature references based on $num
				for (my $i = 0; $badflag == 0 && $i < $bracketnum; $i++) {
					increaseDepth();

					my $textatnum = "";
					$featuresvalid[$feaiter] = 1;
					
					#Cycle the lines and search lines for references
					for (my $funiter = 0; $badflag == 0 && $funiter < scalar @{$featureslist[$feaiter]}; $funiter++) {
					
						my $text = ${$featureslist[$feaiter]}[$funiter];

						#re-sample
						if (!testLineForKeywords($text, $features[$feaiter])) {
							lineCount(12);
							$text = searchForReferences($text, $features[$feaiter]);					
							$textatnum = $textatnum . $text;
						}
					}

					$featuresvalid[$feaiter] = 0;
					
					if ($textatnum ne "" && (($lastlevelflag == 1 && $insingleline[$currentdepth] == 0) ||
					(defined $insingleline[$currentdepth+1] && $insingleline[$currentdepth+1] == 1 && $insingleline[$currentdepth] == 0))) {
						#TODO: Check: Which case needs this?
						#$textatnum =~ s/^/$currentindent[$currentdepth]/;
						#$text =~ s/\n/\n$currentindent[$currentdepth]/g;
						#$text = $currentindent[$currentdepth] . $text;
					}
					
					$replacetext = $replacetext . $textatnum;
					
					decreaseDepth();
				}

				$text =~ s/^([^\S\n]*)//;

				$referencename = fixBracketsForRegEx($referencename);
				
				#Simple replacement if the feature is at the beginning of the line
				if($text =~ /^([^\S\n]*)\$\{$referencename\}([^\S\n]*)/) {
					$replacetext =~ s/\n$//;
					$text =~ s/(^|([^\\]))\$\{$referencename\}/$replacetext/;
					#$text =~ s/\n$//;
				}
				
				#Feature anywhere else
				else {
					$replacetext =~ /^([^\S\n]*)/;
					my $savespace = $1;
					$replacetext =~ s/^([^\S\n]*)//;
					$replacetext =~ s/(\s*)$//;

					if ($text =~ /(^|([^\\]))\$\{$referencename\}/) {
						my $end = $9;
						if (!defined $end) {
							$end = "";
						}
						$text =~ s/(^|([^\\]))\$\{$referencename\}/$1$replacetext$end/;
					}
										
					$text = $savespace.$text;
				}
				$referencereplaced = 1;
				$featuresparamsvalid[$feaiter]--;
			}

					
			if ($currentlastlevelflag == 0) {
				$lastlevelflag = 0;
			}
			$text =~ s/\\$features[$feaiter]/$features[$feaiter]/g;
			$text =~ s/^([\s]*)\\\/\/\//$1\/\/\//g;
			$text =~ s/^([\s]*)\\value/$1value/g;
			$text =~ s/^([\s]*)\\variable/$1variable/g;
			$text =~ s/^([\s]*)\\add/$1add/g;
			$text =~ s/^([\s]*)\\remove/$1remove/g;
			$text =~ s/^([\s]*)\\assert/$1assert/g;

		}
	}
	return $text;
}

# GENERATION PHASE: Replace all feature references
sub replaceFeatureReferencesIR {
	my $text = $_[0];
	return $text;
	for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
		while ($text =~ /((^|([^\\]))(\$\{))($features[$feaiter])(([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\})/) {
			$text =~ s/((^|([^\\]))(\$\{))($features[$feaiter])(([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\})/$1_F$feaiter$6/;
		}
	}	
	return $text;
}



# GENERATION PHASE: Replace all feature references
sub replaceFeatureReferencesNew {

	if ($dotcounter >= 10) {
		printG (2, ".");
		$dotcounter = 0;
	}
	$dotcounter++;
	
	my $text = $_[0];
	my $infeature = $_[1];
	my $currentlastlevelflag = 1;
	while ($text =~ /(^|([^\\]))\$\{_F([\d])(([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\})/) {
		my $feaiter = $3;
				
		#Check for no recursion
		if ($recursionflag == 0) {
			if ($infeature eq $features[$feaiter]) {
				printerror ("CO", "", "$infeature", "$infeature has recursion. Either turn on recursion flag or remove it completely.");
			}
		}
		
		if ($featuresvalid[$feaiter] == 1) {
			printerror ("CP", "", "$features[$feaiter]", "$features[$feaiter] has circular recursion. Either turn on recursion flag or remove it completely.");
		}
		
		printG (3, "$features[$feaiter] reference found.\n");
			
		#Work on spacing
		if ($currentlastlevelflag == 1 && $text =~ /^([^\S\n]*)/) {
		
			my $space = $1;
			#if ($infeature ne "" && $space =~ /^([\t])([^\S\n]*)/)
			#	$space = $2;
			#
			$currentindent[$currentdepth] = $currentindent[$currentdepth] . $space;
		}
		$currentlastlevelflag = 0;
		
		my $bracketnum;
		my @parameterlist;
		#Type 1 is ${parameter}, see parameters if needed
		if ($text =~ /(^|([^\\]))\$\{_F([\d])([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\}/) {
			if (defined $5 && scalar @{$featuresparams[$feaiter]} != 0) {
				@parameterlist = split(",", $5);
				for (my $i = 0; $i < scalar @parameterlist; $i++) {
					$parameterlist[$i] =~ s/^\s+|\s+$//g;
					$parameterlist[$i] = replaceGenesisNamesTop($parameterlist[$i], $infeature, 0);

				}
			}
			
		
			if (defined $7) {
			$bracketnum = $7;
			}
			if (!defined $bracketnum) {
				$bracketnum = 1;
			}
		}
		${$featuresparameterlist[$feaiter]}[$featuresparamsvalid[$feaiter]] = \@parameterlist;
		
		$featuresparamsvalid[$feaiter]++;

		if (scalar @parameterlist > scalar @{$featuresparams[$feaiter]}) {
			printerror ("XS", "", $text, "Too many parameters in this feature.");
		}
		elsif (scalar @parameterlist < scalar @{$featuresparams[$feaiter]}) {
			printerror ("XT", "", $text, "Too few parameters in this feature.");
		}
		#If target code, give an error if it is a parameter in brackets
		if ($currentdepth == 1){
			if ($bracketnum =~ /^[$generegex\d\s]*$/) {
			}
			else {
				for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
					if ($parametersfeature[$pariter] eq "" && $bracketnum =~ /^\$\{$parameters[$pariter]\}$/) {
						printerror ("BH", "", $text, "Feature repetition value not allowed in target code.");
					}
				}
			}
		}
		
		#Added during May 27 reordering
		#Replace names in brackets
		$bracketnum = replaceGenesisNamesTop($bracketnum, $infeature, 0);
		
		#Evaluate
		if (teststringismath($bracketnum)) {
			$bracketnum = eval($bracketnum);
		}
		else {
			printerror ("G", "", $text, "Feature repetition value/number not valid.");
		}

		my $replacetext = generateOnDemand($text, $bracketnum, $feaiter);
		#Do that many feature references based on $num
		

		#Do the replacement, type 1 is brackets	
		$text =~ s/^([^\S\n]*)//;

		#Simple replacement if the feature is at the beginning of the line
		if($text =~ /^([^\S\n]*)\$\{_F([\d])([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\}([^\S\n]*)$/) {
			$replacetext =~ s/\n$//;
			$text =~ s/(^|([^\\]))\$\{_F([\d])([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\}/$replacetext/;
			#$text =~ s/\n$//;
		}
		
		#Feature anywhere else
		else {
			$replacetext =~ /^([^\S\n]*)/;
			my $savespace = $1;
			$replacetext =~ s/^([^\S\n]*)//;
			$replacetext =~ s/(\s*)$//;
			
			if ($text =~ /(^|([^\\]))\$\{_F([\d])([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\}/) {
				my $end = $9;
				if (!defined $end) {
					$end = "";
				}
				$text =~ s/(^|([^\\]))\$\{_F([\d])([^\S\n])*(\((.*)\))?[^\S\n]*(\[[^\S\n]*(.*)[^\S\n]*\])?\}/$1$replacetext$end/;
			}
			
			$text = $savespace.$text;
		}

		$featuresparamsvalid[$feaiter]--;
	}
	if ($currentlastlevelflag == 0) {
		$lastlevelflag = 0;
	}
		
	#for (my $feaiter = 0; $badflag == 0 && $feaiter < scalar @features; $feaiter++) {
	#	$text =~ s/\\$features[$feaiter]/$features[$feaiter]/g;
	#	$text =~ s/^([\s]*)\\\/\/\//$1\/\/\//g;
	#	$text =~ s/^([\s]*)\\value/$1value/g;
	#	$text =~ s/^([\s]*)\\variable/$1variable/g;
	#	$text =~ s/^([\s]*)\\add/$1add/g;
	#	$text =~ s/^([\s]*)\\remove/$1remove/g;
	#	$text =~ s/^([\s]*)\\assert/$1assert/g;
	
	return $text;
}
# GENERATION PHASE: Replace all genloops
sub replaceGenloops {
	my $text = $_[0];
	my $infeature = $_[1];
	my $currentlastlevelflag = 1;
	# Parse out genloop first
	if ($text =~ /(^|^[^\w\\])genloop/) {
		if ($text =~ /(^|^[^\w\\])genloop[\s]*([\w]*):([$generegex]*):([$generegex]*)(:[$generegex]*)? *([\w]*)[^\S\n]*/) {
			my $var = $2;
			my $valueStart = $3;
			my $valueEnd = $4;
			my $valueStride;
			my $id = $6;
			if (defined $5) {
				$valueStride = $5;
				$valueStride =~s/^://;
			}
			if (!defined $valueStride) {
				$valueStride = 1;
			}
			
			#Added during May 27 reordering
			$valueStart = replaceGenesisNamesTop($valueStart, $infeature, 0);		
			$valueEnd = replaceGenesisNamesTop($valueEnd, $infeature, 0);
			$valueStride = replaceGenesisNamesTop($valueStride, $infeature, 0);
			
			if (teststringismath($valueStart)) {
				$valueStart = eval($valueStart);
			}
			else {
				printerror ("AG", "", "$valueStart", "valueStart not fully evaluated.");
			}
			
			if (teststringismath($valueEnd)) {
				$valueEnd = eval($valueEnd);
			}
			else {
				printerror ("AH", "", "$valueEnd", "valueEnd not fully evaluated.");
			}
			
			if (teststringismath($valueStride)) {
				$valueStride = eval($valueStride);
			}
			else {
				printerror ("AI", "", "$valueStride", "valueStride not fully evaluated.");
			}
			lineCount(11);
			lineCount(21);
			my $replacetext = "";
			# Find the right loop info
			for (my $loopiter = 0; $badflag == 0 && $loopiter < scalar @genloopvar; $loopiter++) {

				if ($genloopid[$loopiter] eq $id) {

					$genloopvalid[$loopiter]++;
					
					#Stride is positive
					if ($valueStride > 0) {
						#Do the genloop
						for (my $loopvariter = $valueStart; $badflag == 0 && $loopvariter <= $valueEnd; $loopvariter = $loopvariter + $valueStride) {
							${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1] = $loopvariter;
							#Iterate through the lines in the genloop
							for (my $funiter = 0; $funiter < scalar @{$genlooplist[$loopiter]}; $funiter++) {
								my $changedtext = ${$genlooplist[$loopiter]}[$funiter];
								#re-sample
								if (!testLineForKeywords($changedtext, $infeature)) {
									lineCount(12);
									$changedtext = searchForReferences($changedtext, $infeature);
									$replacetext = $replacetext . $changedtext;
									#$replacetext = $replacetext . $changedtext . "\n";
								}
							}
							$currentlastlevelflag = 0;
							# Moved to end of for loop, only done once?
							#$replacetext =~ s/[^\S\n]*\n$//;
						}
					}
					
					#Stride is negative
					else {
						#Do the genloop
						for (my $loopvariter = $valueStart; $loopvariter >= $valueEnd; $loopvariter = $loopvariter + $valueStride) {
							${$genloopvalue[$loopiter]}[$genloopvalid[$loopiter]-1] = $loopvariter;
							#Iterate through the lines in the genloop
							for (my $funiter = 0; $funiter < scalar @{$genlooplist[$loopiter]}; $funiter++) {
								my $changedtext = ${$genlooplist[$loopiter]}[$funiter];
								#re-sample
								if (!testLineForKeywords($changedtext, $infeature)) {
									$changedtext = searchForReferences($changedtext, $infeature);
									$replacetext = $replacetext . $changedtext;
									#$replacetext = $replacetext . $changedtext . "\n";
								}
							}
							$currentlastlevelflag = 0;
							# Moved to end of for loop, only done once?
							#$replacetext =~ s/[^\S\n]*\n$//;
						}
					}
					
					$genloopvalid[$loopiter] --;
				}
				lineCount(11);
			}
			#Moved here
			#$replacetext =~ s/^[^\S\n]*//;
			$replacetext =~ s/[^\S\n]*\n$//;
			if ($text =~ /(^|^[^\w\\])genloop[\s]*([\w]*):([$generegex]*):([$generegex]*)(:[$generegex]*)?[\s]*([\w]*)[^\S\n]*/) {
				my $before;
				if (defined $1) {
					$before = $1;
				}
				else {
					$before = "";
				}
				$text =~ s/(^|^[^\w\\])genloop[\s]*([\w]*):([$generegex]*):([$generegex]*)(:[$generegex]*)?[\s]*([\w]*)[^\S\n]*/$before$replacetext/;
			}
			else {
				printerror ("ZZV", "", "$text", "Do not think this should happen. Tell Alton if it does.");
			}
			#$text =~ s/\n$//;
		}
		elsif ($text =~ /(^|^[^\w\\])genloop[\s]*(([$referegex]*)[\s]*(==|>=|<=|>|<|!=)[\s]*([$referegex]*)) *([\w]*)[^\S\n]*/) {
			my $condition = $2;
			my $id = $6;
			my $replacetext = "";
			#PROBLEM: scoping means condition stays the same...?
			#No longer a problem due to genmath
			for (my $loopiter = 0; $loopiter < scalar @genloopvar; $loopiter++) {
				if ($genloopid[$loopiter] eq $id){
					my $newcondition = replaceGenesisNamesTop($genloopinequality[$loopiter], $infeature, 1);
					while (evaluateboolean($newcondition, $infeature)) {
				
						for (my $funiter = 0; $funiter < scalar @{$genlooplist[$loopiter]}; $funiter++) {
							my $changedtext = ${$genlooplist[$loopiter]}[$funiter];
							#re-sample
							if (!testLineForKeywords($changedtext, $infeature)) {
								$changedtext = searchForReferences($changedtext, $infeature);
								$replacetext = $replacetext . $changedtext;
							}
						}
						$currentlastlevelflag = 0;
						$newcondition = replaceGenesisNamesTop($genloopinequality[$loopiter], $infeature, 1);
					}
				}
			}
			$replacetext =~ s/\n$//;
			$text =~ s/(^|^[^\w\\])genloop[\s]*(([$referegex]*)[\s]*(==|>=|<=|>|<|!=)[\s]*([$referegex]*)) *([\w]*)[^\S\n]*/$1$replacetext/;
			#$text =~ s/\n$//;
		}
	}
	if ($currentlastlevelflag == 0) {
		$lastlevelflag = 0;
	}
	$text =~ s/\\genloop/genloop/g;
	return $text;
}
# GENERATION PHASE: Replace all genifs
sub replaceGenifs {
	my $text = $_[0];
	my $infeature = $_[1];
	my $currentlastlevelflag = 1;
	my $geniffound = 0;
	my $genifreplaced = 0;
	if ($text =~ /(^|^[^\w\\])genif ([\d]*)[\s]*$/) {
		$geniffound = 1;
		my $id = $2;
		
		#Added during May 27 reordering
		for (my $ifiter = 0; $badflag == 0 && $ifiter < scalar @genifinequality; $ifiter++) {
			if ($genifid[$ifiter] eq $id){
				#If the genif area has not be evaluated yet or if it is the first
				if ($geniftype[$ifiter] == 0) {
					$inagenifflag = 0;
					$genifevaledflag = 0;
				}
				if ($genifevaledflag == 0 || $geniftype[$ifiter] == 0){	
					lineCount(10);
					my $condition = replaceGenesisNamesTop($genifinequality[$ifiter], $infeature, 1);						
					if (evaluateboolean($condition, $infeature)==1) {
						lineCount(20);
						my $replacetext = "";
						for (my $funiter = 0; $funiter < scalar @{$geniflist[$ifiter]}; $funiter++) {
							my $changedtext = ${$geniflist[$ifiter]}[$funiter];
							#re-sample
							if (!testLineForKeywords($changedtext, $infeature)) {
								lineCount(12);
								$changedtext = searchForReferences($changedtext, $infeature);

								$replacetext = $replacetext . $changedtext;
							}
						}
						$replacetext =~ s/\n$//;
						$text =~ s/(^|^[^\w\\])genif ([\d]*)/$1$replacetext/;
						$genifreplaced = 1;
						$currentlastlevelflag = 0;	
						if ($geniftype[$ifiter] == 0 || $geniftype[$ifiter] == 1) {
							$genifevaledflag = 1;
						}
					}
				}
				if ($geniftype[$ifiter] == 2) {
					$geniffound = 0;
				}
			}
		}
		#if the genif is not replaced, remove the genif completely
		if ($genifreplaced == 0) {
			if ($text =~ /(^|^[^\w\\])genif ([\d]*)[\s]*\n/) {
				$text =~ s/(^|^[^\w\\])genif ([\d]*)[\s]*\n/$1/;
			}
			# Happens on fixsingleline now
			else {
				$text =~ s/(^|^[^\w\\])genif ([\d]*)[\s]*/$1/;
				$text =~ s/\n$//;
			}
		}
		$inagenifflag = 1;
	
	}
	if ($geniffound == 0) {
		$inagenifflag = 0;
		$genifevaledflag = 0;
	}
	if ($currentlastlevelflag == 0) {
		$lastlevelflag = 0;
	}
	$text =~ s/\\genif/genif/g;
	return $text;
}
# GENERATION PHASE: Replace all genspaces
sub replaceGenspaces {
	my $text = $_[0];
	my $infeature = $_[1];
	while ($text =~ /(^|^[^\w\\])genspace[\s]*$/) {
		$text =~ s/(^|^[^\w\\])genspace[\s]*$/\n/;
	}

	$text =~ s/\\genspace/genspace/g;
	return $text;
}
# GENERATION PHASE: Replace all gentabs
sub replaceGentabs {
	my $text = $_[0];
	my $infeature = $_[1];
	while ($text =~ /(^|[^\w\\])gentab/) {
		$text =~ s/(^|[^\w\\])gentab/$1\t/;
	}

	$text =~ s/\\gentab/gentab/g;
	return $text;
}
# GENERATION PHASE: Replace all genevals
sub replaceGenevals {
	my $text = $_[0];
	my $infeature = $_[1];
	#find geneval
	while ($text =~ /(^|([^\w\\]))geneval[\s]*\(([^\)]*)\)[\s]*$/) {
		my $condition = $3;
		my $replacetext;
		#old thing that geneval did: call eval
		
		if (teststringismath($condition)) {
			$replacetext = eval($condition);
		}
		else {
			$replacetext = searchForReferences($condition, $infeature);
		}
		
		#substitute
		$text =~ s/(^|([^\w\\]))geneval[\s]*\(([^\)]*)\)/$1$replacetext/;
	}
	$text =~ s/\\geneval/geneval/g;
	return $text;
}

##?##?## FEATURE FLOW ##?##?##

# GENERATION PHASE: Search for all feature references
sub searchForReferences {

	my $text = $_[0];
	my $infeature = $_[1];
	
	increaseDepth();
	#print "Current Depth++: $currentdepth\n";
	#print "Text1: '$text'\n";

	$text = fixsingleline($text, $infeature);

	$text = replaceGenloops($text, $infeature);
	$text = replaceGenifs($text, $infeature);
	if ($timingflag == 1) {
		if ($replacestarttime == 0 || $replaceendtime > $replacestarttime) {
			$replacestarttime = time;
		}
		else {
			my $newreplacestarttime = time;
			$timereplace = $timereplace + ($newreplacestarttime - $replacestarttime);
			$replacestarttime = $newreplacestarttime;
		}
	}
	
	my $laststring = "";
	
	while ($text =~ /(^|[^\\])(\$\{([^\$\{\}]*)\})/) {
		#Reference found
		my $reference = $2;
		my $referencename = $3;
		#check if we are still in the same place
		if ($laststring eq $text) {
			printerror ("DL", "", $laststring, "Either infinite recursion or an error with the compiler.");
		}
		else {
			$laststring = $text;
		}

		$referencereplaced = 0;
		$text = replaceFeatureReferences($text, $reference, $referencename, $infeature);
		if ($referencereplaced == 0) {
			$text = replaceStoredReferences($text, $reference, $referencename, $infeature);
		}
		if ($referencereplaced == 0) {
			$text = replaceGenesisNames($text, $reference, $referencename, $infeature, 0);
		}
		if ($referencereplaced == 0) {
			$text = replaceGenevals($text, $infeature);
		}
		if ($referencereplaced == 0) {
			$text = replaceGenspaces($text, $infeature);
		}
		if ($referencecheck == 1 && $referencereplaced == 0) {
			printerror ("DH1", "", $reference, "Reference found with a non-existent Genesis name.");
		}
	}
	$referencereplaced = 0;
	if ($timingflag == 1) {
		if ($replaceendtime > $replacestarttime) {
			my $newreplaceendtime = time;
			$timereplace = $timereplace + ($newreplaceendtime - $replaceendtime);
			$replaceendtime = $newreplaceendtime;
		}
		else {
			$replaceendtime = time;
			$timereplace = $timereplace + ($replaceendtime - $replacestarttime);
		}
	}
	#if ($lastlevelflag == 0) {
	#	$text =~ s/(^|\n)/$1$currentindent[$currentdepth]/g;
	
	# If Lowest level, and not a single line, and there is text
	# or we just got out of a singleline
	# Add indenting
	
	if ($text ne "" && (($lastlevelflag == 1 && $insingleline[$currentdepth] == 0) ||
	  (defined $insingleline[$currentdepth+1] && $insingleline[$currentdepth+1] == 1 && $insingleline[$currentdepth] == 0))) {
		$text =~ s/^/$currentindent[$currentdepth]/;
	}
	
	#$text = replaceGentabs($text, $infeature);
	
	#print "Returning '$text'\n";
	#print "Current Depth--: $currentdepth\n";
	
	decreaseDepth();
		
	return $text;
}
# GENERATION PHASE: Parses generate, returns number of files (sets) to generate
sub parseGenerateLine {
	my $gensetnumber = $_[0];
	my $generate = 0;
	
	#Reset the distributions
	@distributions = ();
	@distributionsvalues = ();
	@distributionsprob = ();
	@distributionsreal = ();
	
	if ($gentouch[$gensetnumber] == 0){
		$generatetouchflag = 0;
	}
	else {
		$generatetouchflag = 1;
	}
	if (looks_like_number($generates[$gensetnumber])) {
		printG (3, $generates[$gensetnumber] . " to be generated... with this distribution set" . "\n");
		$generate = $generates[$gensetnumber];
	}
	else {
		printerror ("B", "", $generates[$gensetnumber], "Number to be distributed invalid: $generates[$gensetnumber].");	
		
	}

	if ($gendistribute[$gensetnumber] =~ /^[\s]*,/ ||
	$gendistribute[$gensetnumber] =~ /,[\s]*,/ || $gendistribute[$gensetnumber] =~ /,[\s]*$/) {
		printwarning ("WF", "", $gendistribute[$gensetnumber], "This line contains an empty distribution.");
	}
	my @distributiontemp = split(",", $gendistribute[$gensetnumber]);
	my $bracketflag = 0;
	my $joinskip = 0;
	my @distribution;

	
	my $globalandlocal = scalar @globaldistributions + scalar @localdistributions;
	for(my $disiter = 0; $disiter < scalar @distributiontemp; $disiter++) {
		
		if (!defined $distribution[$disiter-$joinskip]) {
			$distribution[$disiter-$joinskip] = $distributiontemp[$disiter];
		}
		else {
			$distribution[$disiter-$joinskip] = $distribution[$disiter-$joinskip].",".$distributiontemp[$disiter];
		}
		printG (3, " Distributions " . ($disiter-$joinskip). ": '". $distribution[$disiter-$joinskip]. "'\n");
		
		#I do not think ordering needs fixing here. Error M/O detects order
		$bracketflag++ while ($distributiontemp[$disiter] =~ /\{/g);
		$bracketflag-- while ($distributiontemp[$disiter] =~ /\}/g);
		
		if ($bracketflag >= 1) {
			$joinskip++;
		}
	}
	for(my $disiter = 0; $disiter < scalar @distribution; $disiter++) {
		handleDistribution($distribution[$disiter],1, "",1);
	}
	for(my $disiter = 0; $disiter < scalar @localdistributions; $disiter++) {
		handleDistribution($localdistributions[$disiter],0, "",1);
	}
	
	return $generate;
}
# GENERATION PHASE: Add spacing to line based on depth
sub adddepthspacing {
my $distline = $_[0];

my $output = "";	
for (my $a = 0; $a < $currentdepth; $a++) {
	$output = $output . " ";
}

$output = $output . $distline;
return $output;
}
# GENERATION PHASE: Sample the global section, returns if it is still enumerating
sub sampleglobal {
	my $lastiteration = $_[0];

	#update enum
	my $i = 0;
	my $updated = 0;
	for ($i = scalar @globalenum-1; $updated == 0 && $i >= 0; $i--) {
		for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
			if ($globalcodelines[$globalenum[$i]] =~ /^value $parametersnumber[$pariter]$/ && defined ${$parameterscounters[$currentdepth]}[$pariter]) {
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {
						for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]} && $updated == 0; $disiter2++) {
							if (${$distributionsvalues[$disiter]}[$disiter2] eq ${$parameterscounters[$currentdepth]}[$pariter]) {
								if ($disiter2+1 != scalar @{$distributionsvalues[$disiter]}) {
									${$parameterscounters[$currentdepth]}[$pariter] = ${$distributionsvalues[$disiter]}[$disiter2+1];
									${$parameterssampled[$currentdepth]}[$pariter] = 1;
									
									printG (3, "$parameters[$pariter] replace to ${$parameterscounters[$currentdepth]}[$pariter] \n");
	
									#removing header lines sampled in features
									#as long as there are still lines to remove, and not removed too many lines, and there are still more feature samples than program samples
									for (my $j = scalar @globalreport-1; scalar @headertemplines > 0 && $j >= 0 && $globalreport[$j] >= $globalenum[$i] ; $j--) {
										splice(@headertemplines, scalar @headertemplines-1, 1);
									}
									
									if ($parametersreportflag[$pariter]==1 && $parametersfullflag[$pariter]==1) {
										$valuereportedflag = 1;
										reportvalue($pariter);
									}
									$updated = 1;
								}
							}
						}
					}
				}
			}
		}
	}
		
	#If it is the last iteration and there is no more enum, stop sampling
	#Only sample if its not last iteration, or if something updated
	if ($lastiteration == 0 || $updated == 1) {
	
		#figure out where to continue processing.
		#$i+1, cause it goes one over before checking updated
		#+1 because the same line should not be run twice
		my $startglobal;
		if ($updated == 1) {
			$startglobal = $globalenum[$i+1]+1;
		}
		elsif ($updated == 0) {
			@headerprogramtemplines = ();
			$startglobal = 0;
			
		}
		else {
			printerror ("ZZW", "", "Updated != 0 or 1 sanity" , "Something is off with the compiler. Tell Alton.");
		}

		for (my $j = scalar @globaldist-1; $j >= 0 && $startglobal <= $globaldist[$j] && $distvalidlocality[$currentdepth] < scalar @distributions; $j--) {
			splice(@distributions, scalar @distributions-1, 1);
			splice(@distributionsvalues, scalar @distributionsvalues-1, 1);
			splice(@distributionsprob, scalar @distributionsprob-1, 1);
			splice(@distributionsreal, scalar @distributionsreal-1, 1);
		}
		
		for (my $funiter = $startglobal; $funiter < scalar @globalcodelines; $funiter++) {
			my $text = $globalcodelines[$funiter];
			#re-sample
			if (!testLineForKeywords($text, "global", 0)) {	
				$text = searchForReferences($text, "global", 0);
			}
		}
	}
	return $updated;
}
# GENERATION PHASE: Sample the program section, returns if it is still enumerating 
sub sampleprogram {
	my $lastiteration = $_[0];
	
	#update enum
	my $i = 0;
	my $updated = 0;
	for ($i = scalar @programenum-1; $updated == 0 && $i >= 0; $i--) {
		for (my $pariter = 0; $pariter < scalar @parameters; $pariter++) {
			if ($programcodelines[$programenum[$i]] =~ /^value $parametersnumber[$pariter]$/ && defined ${$parameterscounters[$currentdepth]}[$pariter]) {
				for (my $disiter = 0; $disiter < scalar @distributions; $disiter++) {
					if ($distributions[$disiter] eq $parametersdistvar[$pariter]) {
						for (my $disiter2 = 0; $disiter2 < scalar @{$distributionsvalues[$disiter]} && $updated == 0; $disiter2++) {
							if (${$distributionsvalues[$disiter]}[$disiter2] eq ${$parameterscounters[$currentdepth]}[$pariter]) {
								if ($disiter2+1 != scalar @{$distributionsvalues[$disiter]}) {
									${$parameterscounters[$currentdepth]}[$pariter] = ${$distributionsvalues[$disiter]}[$disiter2+1];
									${$parameterssampled[$currentdepth]}[$pariter] = 1;

									printG (3, "$parameters[$pariter] replace to ${$parameterscounters[$currentdepth]}[$pariter] \n");
									
									#removing header lines sampled in features
									#as long as there are still lines to remove, and not removed too many lines, and there are still more feature samples than program samples
									for (my $j = scalar @programreport-1; scalar @headerprogramtemplines > 0 && $j >= 0 && scalar @headerprogramtemplines > scalar @programreport; $j--) {										
										splice(@headerprogramtemplines, scalar @headerprogramtemplines-1, 1);
									}
									
									#removing header lines sampled in program
									#as long as there are still lines to remove, and not removed too many lines, and the report line is after (or the same as) the enum changed line
									for (my $j = scalar @programreport-1; scalar @headerprogramtemplines > 0 && $j >= 0 && $programreport[$j] >= $programenum[$i] ; $j--) {
									
										splice(@headerprogramtemplines, scalar @headerprogramtemplines-1, 1);
									}
									
									if ($parametersreportflag[$pariter]==1 && $parametersfullflag[$pariter]==1) {
										$valuereportedflag = 1;
										reportvalue($pariter);
									}
									$updated = 1;
								}
							}
						}
					}
				}
			}
		}
	}
	
	#If it is the last iteration and there is no more enum, stop sampling
	#Only sample if its not last iteration, or if something updated
	if ($lastiteration == 0 || $updated == 1) {
	
		#figure out where to continue processing.
		#$i+1, cause it goes one over before checking updated
		#+1 because the same line should not be run twice
		my $startprogram;
		if ($updated == 1) {
			$startprogram = $programenum[$i+1]+1;
		}
		elsif ($updated == 0) {
			@headerprogramtemplines = ();
			$startprogram = 0;
		}
		else {
			printerror ("ZZX", "", "Updated != 0 or 1 sanity" , "Something is off with the compiler. Tell Alton.");
		}

		for (my $j = scalar @programdist-1; $j >= 0 && $startprogram <= $programdist[$j] && $distvalidlocality[$currentdepth] < scalar @distributions; $j--) {
			splice(@distributions, scalar @distributions-1, 1);
			splice(@distributionsvalues, scalar @distributionsvalues-1, 1);
			splice(@distributionsprob, scalar @distributionsprob-1, 1);
			splice(@distributionsreal, scalar @distributionsreal-1, 1);
		}

		for (my $funiter = $startprogram; $funiter < scalar @programcodelines; $funiter++) {
			my $text = $programcodelines[$funiter];
			#re-sample
			if (!testLineForKeywords($text, "program", 0)) {	
				$text = searchForReferences($text, "program", 0);
			}
		}
	}
	else {
		while ($distvalidlocality[$currentdepth] != scalar @distributions) {
			splice(@distributions, scalar @distributions-1, 1);
			splice(@distributionsvalues, scalar @distributionsvalues-1, 1);
			splice(@distributionsprob, scalar @distributionsprob-1, 1);
			splice(@distributionsreal, scalar @distributionsreal-1, 1);
		}
	}

	return $updated;
}
# GENERATION PHASE: Report value to beginning of file
sub reportvalue {
	my $pariter= $_[0];
	my $line = "Set value " . $parameters[$pariter]. ": ".${$parameterscounters[$currentdepth]}[$pariter]. "\n";
	$headerprogramtemplines[scalar @headerprogramtemplines] = $reportcharacter;
	for (my $a = 0; $a < $currentdepth; $a++) {
		 $headerprogramtemplines[scalar @headerprogramtemplines-1] = $headerprogramtemplines[scalar @headerprogramtemplines-1] . " ";
	}
	$headerprogramtemplines[scalar @headerprogramtemplines-1] = $headerprogramtemplines[scalar @headerprogramtemplines-1] . $line;
	
}
# GENERATION PHASE: Report variable to beginning of file
sub reportvariable {
	my $variter= $_[0];
	my $varnametouse= $_[1];
	my $line = "Set variable " . $variables[$variter]. ": ". $varnametouse.${$variablescounters[$currentdepth]}[$variter]. "\n";
	$headerprogramtemplines[scalar @headerprogramtemplines] = $reportcharacter;
	for (my $a = 0; $a < $currentdepth; $a++) {
		 $headerprogramtemplines[scalar @headerprogramtemplines-1] = $headerprogramtemplines[scalar @headerprogramtemplines-1] . " ";
	}
	$headerprogramtemplines[scalar @headerprogramtemplines-1] = $headerprogramtemplines[scalar @headerprogramtemplines-1] . $line;	
}

# GENERATION PHASE: Iterate through the target code, making feature replacements as necessary
sub iterateThroughTargetCode {
	printG (0, " Working..");
	#For each target code line
	for (my $linesiter = 0; $badflag == 0 && $linesiter < scalar @templateproglines; $linesiter++) {
		my $text = $templateproglines[$linesiter];
		
		lineCount(12);
		#Perform text replacements
		increaseDepth();
		
		if ($timingflag == 1) {
			$replacestarttime = time;
		}
		
		while ($badflag == 0 && $text =~ /(^|[^\\])(\$\{([^\$\{\}]*)\})/) {
			my $reference = $2;
			my $referencename = $3;
			$referencereplaced = 0;
			
			checkTemplateValues($referencename);
			###$referencename = replaceGenesisNamesTop($referencename, "", 0);
			$text = replaceFeatureReferences($text, $reference, $referencename, "", 0);
			if ($referencereplaced == 0) {
				$text = replaceStoredReferences($text, $reference, $referencename, "", 0);
			}
			if ($referencecheck == 1 && $referencereplaced == 0) {
				printerror ("DD", "", $reference, "Reference found, no feature has this Genesis name.");
			}
		}

		if ($timingflag == 1) {
			$replaceendtime = time;
			$timereplace = $timereplace + ($replaceendtime - $replacestarttime);
		}
		
		if (($lastlevelflag == 1 && $insingleline[$currentdepth] == 0) ||
		  (defined $insingleline[$currentdepth+1] && $insingleline[$currentdepth+1] == 1 && $insingleline[$currentdepth] == 0)
		  && $text ne '') {
			$text =~ s/^/$currentindent[$currentdepth]/;
			#$text =~ s/\n/\n$currentindent[$currentdepth]/g;
			#$text = $currentindent[$currentdepth] . $text;
		}
		
		$currentindent[$currentdepth] = "";
		decreaseDepth();
		
		#If the line is blank and ignore vertical space, ignore line
		if ($ignorevertspaceflag == 1 && $text =~ /^[\s]*$/) {
			printG (3, "Do not include this line");
		}
		
		#Otherwise it is a normal line and just place it normally
		else {
			$templines[scalar @templines] = $text;
		}
	}
	printG (2, " \n");
}
# GENERATION PHASE: Print single instance of target code to single file
sub printtofile {
	#Formerly called addheader
	my $geniter = $_[0];
	my $enumeratenumber = $_[1];
	open (OUTPUTFILE, ">:crlf", $outname1.$geniter."_".$enumeratenumber.$outname2) or die "cannot read new file: $!";

	if ($headerflag == 1) {
		print OUTPUTFILE "$reportcharacter$reportcharacter"." Genesis Program:  $filename\n";
		
		if (defined $filename2) {
			print OUTPUTFILE "$reportcharacter$reportcharacter"." Template Program: $filename2\n";
		}
		
		print OUTPUTFILE "$reportcharacter$reportcharacter"."File created: $outname1$geniter"."_"."$enumeratenumber$outname2 \n";
		if ($valuereportedflag == 1) {
			print OUTPUTFILE "\n$reportcharacter"."Sampled Reported Values:\n";
		}
		
		
		for (my $linesiter = 0; $linesiter < scalar @headertemplines; $linesiter++) {
			my $text = $headertemplines[$linesiter];
			print OUTPUTFILE $text;
		}				
		for (my $linesiter = 0; $linesiter < scalar @headerprogramtemplines; $linesiter++) {
			my $text = $headerprogramtemplines[$linesiter];
			print OUTPUTFILE $text;
		}
	}
	
	
	for (my $linesiter = 0; $linesiter < scalar @templines; $linesiter++) {
		my $text = $templines[$linesiter];
		print OUTPUTFILE $text;
	}
	print OUTPUTFILE "\n";
	print OUTPUTFILE "\n";	
	
	close (OUTPUTFILE);
	
	
}

##?##?## REGULAR FLOW ##?##?##

# PARSING PHASE: Top Level Parsing Phase function
sub phase1Parse {
	if ($timingflag == 1) {
		$starttime = time;
	}
	TEST: while ($checkoneheaderflag == 0) {
		my $text = <GENPROGFILE>;
		$linenumber++;
		
		#$/ = "\r\n";
		chomp($text);
		my $keyword;
		my $info;
		($keyword, $info) = split(" ", $text, 2);

		if (defined $keyword and $keyword eq "begin" and defined $info and $info eq "genesis") {
		
			printP (2, "Begin genesis!\n");

			my @temp;
			$namesforlocality[$parsebracketcounter+1] = \@temp;
			
			while ($checkoneheaderflag == 0) {
				my $text = <GENPROGFILE>;
				
				parseGenesisLine($text);			
			}
			if ($checkoneheaderflag == 0) {
				printerror ("AC", "", "End of header", "No end genesis line.");
			}
			if ($programexistsflag == 0) {
				printwarning ("WH", "", "End of header", "No program segment.\n");
			}
			if ($globalexistsflag == 0) {
				printwarning ("WJ", "", "End of header", "No global segment.\n");
			}
		}
		elsif ($text =~ /^\#/) {
			printP (2, "Ignore comment line, before language barriers.\n");
		}
		elsif ($text =~ /^[\s]*$/) {
			printP (2, "Ignore whitespace line, before language barriers.\n");
		}
		else {
			printerror ("CJ", "", "Before header", "First non-whitespace line is not 'begin genesis'.");
		}
	}
	if ($timingflag == 1) {
		$endtime = time;
		$timeparse = $endtime - $starttime;
	}
	printP (2, "End parse!\n\n");
	$parsingflag = 0;
	printeverything;

	if ($filename2 eq "") {	
		TEST2: while (my $text = <GENPROGFILE>) {
			#TODO: if we want an IR 
			#$text = replaceFeatureReferencesIR($text);
			$templateproglines[scalar @templateproglines] = $text;
		}
	}
	else {
		while (my $text = <TEMPLATEPROGFILE>) {
			#TODO: if we want an IR 
			#$text = replaceFeatureReferencesIR($text);
			$templateproglines[scalar @templateproglines] = $text;
		}
		close (TEMPLATEPROGFILE);
	}
	close (GENPROGFILE);
}
# GENERATION PHASE: Top Level Generation Phase function
sub phase2Generate {
	if ($generateflag == 1) {
	
		if (! (-d "./GeneratedInstancePrograms")) {
			#Open Instance Program
			mkdir("./GeneratedInstancePrograms", 0700) unless(-d "./GeneratedInstancePrograms");
		}
		chdir("./GeneratedInstancePrograms") or die "cannot chdir ./GeneratedInstancePrograms\n";

		if (! (-d "./$outDir")) {
			#Open Instance Program
			mkdir("./$outDir", 0700) unless(-d "./$outDir");
			chdir("./$outDir") or die "cannot chdir ./$outDir\n";
		}
		else {
			$foldercounter++;
			while (-d "./$outDir$foldercounter") {
				$foldercounter++;
			}
			
			mkdir("./$outDir$foldercounter", 0700) unless(-d "./$outDir$foldercounter");
			chdir("./$outDir$foldercounter") or die "cannot chdir ./$outDir$foldercounter\n";
			
		}
		#Order of operations stuff (OOO)
	
		#This is implemented for now
		#OOO1: Global is global for each line
		#Parse the distributions in the global line
		#Go through globals
		#Generate the number indicated
		#Enumerate global as necessary
		
		#OOO2: Global is sampled once for everything
		#That means we cannot have distributions in the generate line (with them, there is no knowledge of which distribution to use)
		
		#OOO3: Old method
		#Enumerate global for everything
		#The number indicated is the final number of programs, i.e., enumerated global should be 5 if instance programs is 5
		#Gives user flexibility
		#Problem is non enumerated values will mess things up and screws up the idea of ordering
		my $generateupto = 1;	#Generate up to this value
		#FOR EACH GENERATE LINE
		for (my $gensiter = 0; $gensiter < scalar @generates; $gensiter++) {
			if ($timingflag == 1) {
				$starttime = time;
			}
			@headertemplines= ();
		
			#Get the number of files (sets) to generate, parse all the dists
			my $generate = parseGenerateLine($gensiter);
			
			#setup global counters for this generate line (with this set of dists)
			setupGlobalCounters();
			#setupparamstartcounters;
			
			#Total number of sets
			$setcounter = $setcounter + $generate;
			
			#the number of valid distributions at this point
			$distvalidlocality[$currentdepth] = scalar @distributions;
			
			my $stillenumeratingglobal = 1;
			my $firstiteration = 1;
			
			#FOR EACH STILL ENUMERATING
			
			while ($stillenumeratingglobal == 1 && 
			(scalar @globalenum > 0 || $firstiteration == 1) ) {
				@headerprogramtemplines = ();

				#Returns whether we're still enumerating 
				if ($gensiter == scalar @generates) {
					$stillenumeratingglobal = sampleglobal(1);
				}
				else {
					$stillenumeratingglobal = sampleglobal(0);

				}
				
				if (scalar @globalenum == 0) {
					$stillenumeratingglobal = 0;
				}
				if ($firstiteration == 1 || $stillenumeratingglobal == 1) {
					if ($firstiteration == 1) {
						$stillenumeratingglobal = 1;
					}
					#not the first iteration
					$firstiteration = 0;
					
					#Generate from genstart to generateupto
					my $genstart = $generateupto;
					$generateupto = $generateupto + $generate;
					printG (2, "Generating " . $generate . " now!" . "\n");
					
					#Transfer all the globally sampled lines to its own array and clear old one
					for (my $i = 0; $i < scalar @headerprogramtemplines; $i++) {
						$headertemplines[scalar @headertemplines] =$headerprogramtemplines[$i];
					}
					@headerprogramtemplines = ();

					#Total global distributions.
					$distvalidlocality[$currentdepth] = scalar @distributions;

					#Line moved to before first sample
					#setupGlobalCounters();
					
					my $enumeratenumber = 1;
					my $overflowflag = 0;
					
					#FOR EACH INDIVIDUAL FILE
					
					for (my $geniter = $genstart; $overflowflag == 0 && $geniter < $generateupto+1; $geniter++) {
						#?# April 30: Removed
						#setupparamstartcounters;
						#setupparamlocalcounters;
						
						my $stillenumerating;
						
						#last set, maybe, send a flag. If last set, no need to sample.
						if ($geniter == $generateupto) {
							#might be over the limit
							$stillenumerating = sampleprogram(1);
						}
						else {
							#Regular flow is here
							$stillenumerating = sampleprogram(0);
						}
						
						
						#If we're no longer enumerating, reset the enum counter
						if ($stillenumerating == 0) {
							$enumeratenumber = 1;
						}
						#Else, we are enumerating, increase the number, stick with the old set number
						else {
							$enumeratenumber++;
							$geniter--;
						}
						#Alternative to break. If we are beyond what we are supposed to generate, set overflow flag.
						if ($geniter >=	 $generateupto){
							$overflowflag = 1;
						}
						#else, continue normal processing.
						else {
							$generatecounter++;
							$dotcounter = 10;
							if ($enumeratenumber == 1) {
								printG (2, "\nGenerating #$geniter\n");
							}
							if (scalar @programenum > 0) {
								if ($enumeratenumber != 1) {
									printG (2, "\n");
								}
								printG (2, "  Enumerating #$enumeratenumber\n");
							}
				
							$genbracketcounter = 0;
							
							@templines = ();
							
							iterateThroughTargetCode();					
							
							if ($timingflag == 1) {
								$endtime = time;
								$timecreate = $timecreate + ($endtime - $starttime);
							}
							
							if ($badflag == 0) {
								if ($timingflag == 1) {
									$starttime = time;
								}
							
								printtofile($geniter, $enumeratenumber);
								
								if ($timingflag == 1) {
									$endtime = time;
									$timegen = $timegen + ($endtime - $starttime);
								}
								
							}
							
							else {
								my $removalflag = 0;
								if ($badflag == 1) {
									$removalflag = 1;
									printwarning ("W1", "", "Bad flag", "BAD FLAG 1 - Assert fail\n");
								}
								elsif ($badflag == 2) {
									#Original Action: Delete and retry
									if ($emptyvarlistactionflag == 0) {
										$removalflag = 1;
										printwarning ("W2", "", "Bad flag", "BAD FLAG 2 - Empty Var List\n");
										$duplicatecounter++;
										if ($duplicatecounter == 100) {
											#may be removed later
											printerror ("ZZZ", "", "A", "Way too many duplicates for some reason. Exiting for now to prevent infinite loop.");
										}
									}
									#New Action: Delete and move on
									else {
										$errorlist[scalar @errorlist] = $geniter;
										$errorlist2[scalar @errorlist2] = $enumeratenumber;
										$removalflag = 1;
										$badflag = 0;
									}
								}
								elsif ($badflag == 3 || $badflag == 4) {
									$removalflag = 1;
									$duplicatecounter++;
									if ($duplicatecounter == 100) {
										#may be removed later
										printerror ("AD", "", "A", "Way too many duplicates for some reason. Exiting for now to prevent infinite loop.");
									}
								}
								
								if ($removalflag == 1) {
									$badflag = 0;
									$removalflag = 0;
									unlink $outname1.$geniter."_".$enumeratenumber.$outname2;
								}
								else {
									$duplicatecounter = 0;
								}
						
							}
							
							#printParamlocalcounters;
						}	
					}
					printParamglobalcounters;
				}
			}
		}
	}
	else {
		print "Generate flag off: Nothing to generate.";
	}
	printG (2, " \n");
	
	printfinalreport;
		
}

#Normal flow of the program
if ($printintroflag != 0) {
	print "\n Opening Genesis Version $versionnumber!\n\n";
}
handleArguments();
openOutputFiles();
phase1Parse();
phase2Generate();

exit;